Table 1. Get Full Table
| Number | ContainerName | DateLastTouched | Description | URL |
|---|---|---|---|---|
| 1 | 2pg_cartesian | 2016_08_26__21_27_36 | 2pg cartesian is a framework of optimization algorithms for protein structure prediction. | URL |
| 2 | abricate | 2016_09_05__13_10_17 | Mass screening of contigs for antibiotic resistance genes | URL |
| 3 | abundancebin | 2016_11_13__12_00_44 | 'abundance-based tool for binning metagenomic sequences' | URL |
| 4 | abyss | 2017_03_05__09_28_10 | assembly by short sequences - a de novo, parallel, paired-end sequence assembler | URL |
| 5 | abyss-k128 | 2017_02_19__16_39_36 | None | URL |
| 6 | addrg | 2017_03_13__19_42_20 | None | URL |
| 7 | aenum | 2016_08_30__15_06_10 | Advanced enumerations (compatible with python's stdlib enum), namedtuples, and namedconstants | URL |
| 8 | age-metasv | 2016_05_04__12_08_31 | Optimal alignment of sequences with structural variants (svs), modifiied for metasv integration | URL |
| 9 | agg | 2016_12_29__07_24_22 | gvcf aggregation tool | URL |
| 10 | align_it | 2016_05_19__19_51_28 | Align-it is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions. | URL |
| 11 | alignlib-lite | 2016_09_20__12_47_50 | Simple wrapper around alignlib c++ library for sequence alignment | URL |
| 12 | amos | 2016_05_13__14_03_08 | A modular, open-source whole genome assembler | URL |
| 13 | andi | 2017_01_21__10_34_20 | 'efficient estimation of evolutionary distances' | URL |
| 14 | angsd | 2016_11_27__07_49_23 | "angsd: analysis of next generation sequencing data" | URL |
| 15 | aniso8601 | 2016_09_05__22_06_25 | A library for parsing iso 8601 strings. | URL |
| 16 | ansible | 2016_09_05__08_55_58 | Radically simple it automation | URL |
| 17 | ant | 2017_01_25__23_45_42 | apache ant is a java library and command-line tool that help building software. | URL |
| 18 | antarna | 2016_11_25__07_11_34 | Antarna is a python based implementation of ant-colony optimization of the rna inverse folding problem. | URL |
| 19 | anvio | 2017_01_09__07_53_52 | An interactive analysis and visualization platform for 'omics data | URL |
| 20 | appdirs | 2016_09_05__22_11_18 | A small python module for determining appropriate platform-specific dirs, e.g. a "user data dir". | URL |
| 21 | aragorn | 2016_09_05__09_01_16 | Aragorn, trna (and tmrna) detection | URL |
| 22 | argh | 2016_09_05__22_14_58 | An unobtrusive argparse wrapper with natural syntax | URL |
| 23 | argparse | 2016_09_21__07_05_16 | Python command-line parsing library | URL |
| 24 | argutils | 2016_09_07__19_18_01 | Functions to build matched argument parsers and config files | URL |
| 25 | aria2 | 2016_09_05__09_04_57 | Aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. it supports http/https, ftp, sftp, bittorrent and metalink. | URL |
| 26 | ariba | 2016_12_15__07_20_43 | Ariba: antibiotic resistance identification by assembly | URL |
| 27 | arrow | 2016_09_07__05_23_26 | Better dates and times for python | URL |
| 28 | art | 2017_03_28__06_42_35 | Illumina, 454 and solid read simulator | URL |
| 29 | arvados-cli | 2016_09_05__09_08_59 | Command line interface to arvados, a free and open source platform for big data science | URL |
| 30 | arvados-cwl-runner | 2017_03_28__10_28_07 | Arvados common workflow language runner | URL |
| 31 | arvados-python-client | 2016_11_27__11_23_04 | Python api for arvados, an open source platform for managing and analyzing biomedical big data | URL |
| 32 | asciigenome | 2017_02_11__09_55_24 | Command-line genome browser running from terminal window and solely based on ascii characters | URL |
| 33 | askocli | 2017_03_03__08_00_04 | None | URL |
| 34 | astalavista | 2016_09_05__09_13_50 | Astalavista is a computer program to extract alternative splicing (as) events from a given genomic annotation of exon-intron gene coordinates. by comparing all given transcripts, astalavista detects the variations in their splicing structure and identify all as events (like exon skipping, alternate donor, etc) by assigning to each of them an as code. | URL |
| 35 | atac | 2017_01_10__17_29_16 | "atac is a computational process for comparative mapping between two genome assemblies, or between two different genomes" | URL |
| 36 | augustus | 2016_09_05__09_20_55 | Augustus is a gene prediction program for eukaryotes written by mario stanke and oliver keller. it can be used as an ab initio program, which means it bases its prediction purely on the sequence. augustus may also incorporate hints on the gene structure coming from extrinsic sources such as est, ms/ms, protein alignments and synthenic genomic alignments. | URL |
| 37 | autoconf | 2017_01_12__02_10_16 | A module to implement some of AutoConf macros in pure perl. > License: Perl 5 | URL |
| 38 | autodock-vina | 2016_05_03__22_58_30 | Autodock vina is an open-source program for doing molecular docking | URL |
| 39 | autolog | 2016_09_05__22_35_43 | Quick and easy logging setup | URL |
| 40 | avro | 2016_09_05__22_45_21 | None | URL |
| 41 | avro-python2 | 2016_10_04__14_47_48 | Avro is a serialization and rpc framework. | URL |
| 42 | avro-python3 | 2016_10_04__15_39_43 | Avro is a serialization and rpc framework. | URL |
| 43 | awscli | 2016_09_07__09_41_03 | Universal command line environment for aws | URL |
| 44 | axiome | 2017_02_12__07_49_43 | None | URL |
| 45 | azure-cli | 2017_04_11__17_59_35 | Microsoft azure cross platform command line | URL |
| 46 | backports.csv | 2016_09_06__14_23_30 | Backport of python 3 csv module | URL |
| 47 | backports.unittest_mock | 2016_09_05__22_54_11 | Backports.unittest_mock | URL |
| 48 | baitfisher | 2016_10_20__07_03_51 | the baitfisher-package is a software package for designing hybrid enrichment probes. | URL |
| 49 | bamhash | 2016_09_06__12_55_13 | None | URL |
| 50 | bamtools | 2016_05_15__22_37_50 | C++ api & command-line toolkit for working with bam data | URL |
| 51 | barrnap | 2017_01_27__22_28_00 | Find 5s, 16s and 23s ribosomal rna genes in bacterial contigs | URL |
| 52 | base64 | 2016_03_10__21_42_10 | Encode and decode base64 files | URL |
| 53 | bats | 2016_09_01__13_04_11 | Bash automated testing system | URL |
| 54 | bayescan | 2016_09_07__14_31_53 | Phylogenetics - randomized axelerated maximum likelihood. | URL |
| 55 | bbmap | 2017_03_29__06_29_44 | "bbmap is a short read aligner, as well as various other bioinformatic tools" | URL |
| 56 | bc | 2016_03_10__09_06_26 | An arbitrary precision numeric processing language (calculator) | URL |
| 57 | bcbio-nextgen | 2017_03_29__14_38_28 | Validated, scalable, community developed variant calling, rna-seq and small rna analysis | URL |
| 58 | bcbio-nextgen-vm | 2017_03_29__14_43_46 | Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines | URL |
| 59 | bcbio-prioritize | 2016_09_05__10_41_58 | Prioritize small variants, structural variants and coverage based on biological inputs | URL |
| 60 | bcbio-rnaseq | 2016_11_13__18_09_33 | Report generation for bcbio-nextgen rna-seq runs | URL |
| 61 | bcbio-variation | 2016_09_08__09_13_25 | Toolkit to analyze genomic variation data, built on the gatk with clojure | URL |
| 62 | bcbio-variation-recall | 2016_09_05__11_25_10 | Parallel merging, squaring off and ensemble calling for genomic variants | URL |
| 63 | bcbio_monitor | 2016_09_05__10_37_33 | Bcbio-monitor is an extension of bcbio-nextgen to visualize its progress | URL |
| 64 | bcbiogff | 2016_09_11__07_09_36 | Read and write generic feature format (gff) with biopython integration. | URL |
| 65 | bcbreport | 2016_09_05__23_05_21 | Rmd templates for bcbio-nextgen analysis | URL |
| 66 | bcdoc | 2016_09_05__23_09_23 | None | URL |
| 67 | bcftools | 2017_03_21__10_20_41 | Bcftools is a set of utilities that manipulate variant calls in the variant call format (vcf) and its binary counterpart bcf. all commands work transparently with both vcfs and bcfs, both uncompressed and bgzf-compressed. most commands accept vcf, bgzipped vcf and bcf with filetype detected automatically even when streaming from a pipe. indexed vcf and bcf will work in all situations. un-indexed vcf and bcf and streams will work in most, but not all situations. | URL |
| 68 | bcl2fastq-nextseq | 2017_04_11__17_59_35 | Nextseq .bcl conversion | URL |
| 69 | bd2k-python-lib | 2016_11_27__11_24_44 | The bd2k python module kitchen sink | URL |
| 70 | beagle | 2017_04_06__22_06_37 | Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. | URL |
| 71 | beagle-lib | 2017_03_13__23_22_50 | General purpose library for evaluating the likelihood of sequence evolution on trees | URL |
| 72 | beast | 2017_03_09__18_23_05 | Beast is a cross-platform program for bayesian analysis of molecular sequences using mcmc | URL |
| 73 | beast2 | 2017_03_14__08_06_14 | None | URL |
| 74 | bedops | 2017_03_14__08_36_25 | High-performance genomic feature operations. | URL |
| 75 | bedtools | 2016_10_14__07_04_25 | A powerful toolset for genome arithmetic | URL |
| 76 | besst | 2016_09_06__12_00_30 | Scaffolder for genomic assemblies. | URL |
| 77 | bfc | 2016_09_14__07_03_35 | Bfc is a standalone high-performance tool for correcting sequencing errors from illumina sequencing data. | URL |
| 78 | bgt | 2016_09_14__07_04_04 | Flexible genotype query among 30,000+ samples whole-genome. | URL |
| 79 | bioawk | 2016_12_03__08_12_02 | Bwk awk modified for biological data | URL |
| 80 | biobambam | 2016_11_26__11_30_59 | Tools for early stage alignment file processing | URL |
| 81 | bioblend | 2016_09_01__13_12_24 | A python library for interacting with cloudman and the galaxy api | URL |
| 82 | bioconductor-affy | 2016_09_30__06_38_27 | The package contains functions for exploratory oligonucleotide array analysis. the dependence on tkwidgets only concerns few convenience functions. 'affy' is fully functional without it. | URL |
| 83 | bioconductor-affyio | 2016_09_29__18_23_37 | Routines for parsing affymetrix data files based upon file format information. primary focus is on accessing the cel and cdf file formats. | URL |
| 84 | bioconductor-alpine | 2016_11_17__21_20_25 | Fragment sequence bias modeling and correction for rna-seq transcript abundance estimation. | URL |
| 85 | bioconductor-annotate | 2016_09_16__07_13_19 | Using r enviroments for annotation. | URL |
| 86 | bioconductor-annotationdbi | 2017_03_29__16_52_05 | Provides user interface and database connection code for annotation data packages using sqlite data storage. | URL |
| 87 | bioconductor-annotationforge | 2016_10_25__23_23_06 | Provides code for generating annotation packages and their databases. packages produced are intended to be used with annotationdbi. | URL |
| 88 | bioconductor-aroma.light | 2017_02_17__17_51_11 | None | URL |
| 89 | bioconductor-ballgown | 2016_09_24__07_09_11 | Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. | URL |
| 90 | bioconductor-basic4cseq | 2017_02_04__07_48_27 | Basic4cseq is an r/bioconductor package for basic filtering, analysis and subsequent visualization of 4c-seq data. virtual fragment libraries can be created for any bsgenome package, and filter functions for both reads and fragments and basic quality controls are included. fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | URL |
| 91 | bioconductor-bayespeak | 2016_09_20__12_50_50 | This package is an implementation of the bayespeak algorithm for peak-calling in chip-seq data. | URL |
| 92 | bioconductor-biobase | 2017_03_29__16_51_13 | Functions that are needed by many other packages or which replace r functions. | URL |
| 93 | bioconductor-biocgenerics | 2016_11_03__13_41_33 | S4 generic functions needed by many bioconductor packages. | URL |
| 94 | bioconductor-biocinstaller | 2016_10_08__16_54_51 | This package is used to install and update bioconductor, cran, and (some) github packages. | URL |
| 95 | bioconductor-biocparallel | 2016_10_08__19_17_22 | This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with bioconductor objects. | URL |
| 96 | bioconductor-biocstyle | 2016_10_08__16_57_44 | Provides standard formatting styles for bioconductor pdf and html documents. package vignettes illustrate use and functionality. | URL |
| 97 | bioconductor-biomart | 2016_09_08__00_04_35 | In recent years a wealth of biological data has become available in public data repositories. easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomart provides an interface to a growing collection of databases implementing the biomart software suite (http://www.biomart.org). the package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex sql queries. examples of biomart databases are ensembl, cosmic, uniprot, hgnc, gramene, wormbase and dbsnp mapped to ensembl. these major databases give biomart users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining. | URL |
| 98 | bioconductor-biomformat | 2017_02_05__00_10_22 | This is an r package for interfacing with the biom format. this package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. the design of this api is intended to match the python api and other tools included with the biom-format project, but with a decidedly "r flavor" that should be familiar to r users. this includes s4 classes and methods, as well as extensions of common core functions/methods. | URL |
| 99 | bioconductor-bionet | 2016_11_17__07_07_24 | This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. e.g. p-values obtained from the differential expression of the genes from an affymetrix array are assigned to the nodes of the network. by fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. | URL |
| 100 | bioconductor-biosigner | 2016_09_07__16_53_54 | Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. this package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. the approach can be run in parallel with the pls-da, random forest, and svm binary classifiers. the signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. a galaxy implementation of the package is available within the workflow4metabolomics.org online infrastructure for computational metabolomics. | URL |
| 101 | bioconductor-biostrings | 2016_10_07__16_09_57 | Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | URL |
| 102 | bioconductor-biovizbase | 2016_09_07__03_24_11 | The biovizbase package is designed to provide a set of utilities, color schemes and conventions for genomic data. it serves as the base for various high-level packages for biological data visualization. this saves development effort and encourages consistency. | URL |
| 103 | bioconductor-bsgenome | 2016_11_11__07_07_14 | Infrastructure shared by all the biostrings-based genome data packages | URL |
| 104 | bioconductor-bsgenome.celegans.ucsc.ce6 | 2016_09_06__08_57_35 | Full genome sequences for caenorhabditis elegans (worm) as provided by ucsc (ce6, may 2008) and stored in biostrings objects. | URL |
| 105 | bioconductor-bsgenome.dmelanogaster.ucsc.dm3 | 2016_09_07__13_49_06 | Full genome sequences for drosophila melanogaster (fly) as provided by ucsc (dm3, apr. 2006) and stored in biostrings objects. | URL |
| 106 | bioconductor-bsgenome.ecoli.ncbi.20080805 | 2016_09_08__03_25_49 | Escherichia coli full genomes for several strains as provided by ncbi on 2008/08/05 and stored in biostrings objects. | URL |
| 107 | bioconductor-bsgenome.hsapiens.ucsc.hg19 | 2016_10_03__20_45_45 | Full genome sequences for homo sapiens (human) as provided by ucsc (hg19, feb. 2009) and stored in biostrings objects. | URL |
| 108 | bioconductor-bsgenome.mmusculus.ucsc.mm10 | 2017_01_21__07_45_21 | Full genome sequences for mus musculus (mouse) as provided by ucsc (mm10, jul. dec. 2011) and stored in biostrings objects. | URL |
| 109 | bioconductor-bsgenome.mmusculus.ucsc.mm9 | 2016_10_08__16_45_23 | Full genome sequences for mus musculus (mouse) as provided by ucsc (mm9, jul. 2007) and stored in biostrings objects. | URL |
| 110 | bioconductor-bumphunter | 2016_09_29__20_21_32 | Tools for finding bumps in genomic data | URL |
| 111 | bioconductor-camera | 2016_10_19__20_59_27 | Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, eic correlation based tagging of unknown adducts and fragments | URL |
| 112 | bioconductor-cardinal | 2017_01_15__07_37_04 | Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. | URL |
| 113 | bioconductor-category | 2016_10_26__02_58_15 | A collection of tools for performing category analysis. | URL |
| 114 | bioconductor-cexor | 2016_09_06__10_54_37 | Strand specific peak-pair calling in chip-exo replicates. the cumulative skellam distribution function (package 'skellam') is used to detect significant normalised count differences of opposed sign at each dna strand (peak-pairs). irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'. | URL |
| 115 | bioconductor-cghbase | 2016_10_08__20_36_02 | Contains functions and classes that are needed by arraycgh packages. | URL |
| 116 | bioconductor-cghcall | 2016_09_06__11_09_19 | Calls aberrations for array cgh data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. visualization of profiles is also provided. | URL |
| 117 | bioconductor-chicago | 2017_01_11__16_14_10 | A pipeline for analysing capture hi-c data. | URL |
| 118 | bioconductor-chipseeker | 2016_11_07__22_43_24 | This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among chip peak data sets, and incorporate geo database for user to compare the own dataset with those deposited in database. the comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to tss regions, genomic annotation, distance to tss, and overlap of peaks or genes. | URL |
| 119 | bioconductor-clusterprofiler | 2016_11_13__18_05_38 | This package implements methods to analyze and visualize functional profiles (go and kegg) of gene and gene clusters. | URL |
| 120 | bioconductor-cn.mops | 2017_02_03__23_53_46 | Cn.mops (copy number estimation by a mixture of poissons) is a data processing pipeline for copy number variations and aberrations (cnvs and cnas) from next generation sequencing (ngs) data. the package supplies functions to convert bam files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. therefore, it does not suffer from read count biases along chromosomes. using a bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and poisson distributions, respectively. cn.mops guarantees a low fdr because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in c++. | URL |
| 121 | bioconductor-complexheatmap | 2016_09_06__12_47_23 | Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. here the complexheatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics. | URL |
| 122 | bioconductor-csaw | 2016_12_06__21_38_20 | Detection of differentially bound regions in chip-seq data with sliding windows, with methods for normalization and proper fdr control. | URL |
| 123 | bioconductor-cummerbund | 2017_01_28__22_17_15 | Allows for persistent storage, access, exploration, and manipulation of cufflinks high-throughput sequencing data. in addition, provides numerous plotting functions for commonly used visualizations. | URL |
| 124 | bioconductor-customprodb | 2017_01_15__07_41_08 | None | URL |
| 125 | bioconductor-dada2 | 2016_12_06__21_39_37 | The dada2 package provides "otu picking" functionality, but instead of picking otus the dada2 algorithm exactly infers samples sequences. the dada2 pipeline starts from demultiplexed fastq files, and outputs inferred sample sequences and associated abundances after removing substitution and chimeric errors. taxonomic classification is also available via a native implementation of the rdp classifier method. | URL |
| 126 | bioconductor-deepsnv | 2017_01_28__11_22_09 | This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. the deepsnv algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal snvs. the shearwater algorithm computes a bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters such as local error rates and dispersion and prior knowledge, e.g. from variation data bases such as cosmic. | URL |
| 127 | bioconductor-degreport | 2016_09_07__13_59_56 | Creation of a html report of differential expression analyses of count data. it integrates some of the code mentioned in deseq2 and edger vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene. | URL |
| 128 | bioconductor-deseq | 2016_05_03__23_04_22 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution | URL |
| 129 | bioconductor-deseq2 | 2017_03_29__16_56_02 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | URL |
| 130 | bioconductor-dexseq | 2017_04_03__16_40_31 | The package is focused on finding differential exon usage using rna-seq exon counts between samples with different experimental designs. it provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. the package also provides functions for the visualization and exploration of the results. | URL |
| 131 | bioconductor-diffbind | 2016_09_29__20_33_05 | Compute differentially bound sites from multiple chip-seq experiments using affinity (quantitative) data. also enables occupancy (overlap) analysis and plotting functions. | URL |
| 132 | bioconductor-dirichletmultinomial | 2016_11_01__18_04_32 | Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. this package is an interface to code originally made available by holmes, harris, and quince, 2012, plos one 7(2): 1-15, as discussed further in the man page for this package, ?dirichletmultinomial. | URL |
| 133 | bioconductor-dnacopy | 2016_10_30__07_06_44 | Implements the circular binary segmentation (cbs) algorithm to segment dna copy number data and identify genomic regions with abnormal copy number. | URL |
| 134 | bioconductor-do.db | 2016_09_06__14_44_44 | A set of annotation maps describing the entire disease ontology assembled using data from do | URL |
| 135 | bioconductor-dose | 2016_11_13__18_04_12 | This package implements five methods proposed by resnik, schlicker, jiang, lin and wang respectively for measuring semantic similarities among do terms and gene products. enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data. | URL |
| 136 | bioconductor-dupradar | 2016_09_29__22_05_26 | Duplication rate quality control for rna-seq datasets. | URL |
| 137 | bioconductor-ebimage | 2017_04_11__17_59_35 | Ebimage provides general purpose functionality for image processing and analysis. in the context of (high-throughput) microscopy-based cellular assays, ebimage offers tools to segment cells and extract quantitative cellular descriptors. this allows the automation of such tasks using the r programming language and facilitates the use of other tools in the r environment for signal processing, statistical modeling, machine learning and visualization with image data. | URL |
| 138 | bioconductor-ebseq | 2017_03_29__16_48_49 | Differential expression analysis at both gene and isoform level using rna-seq data | URL |
| 139 | bioconductor-edaseq | 2017_02_21__11_00_56 | None | URL |
| 140 | bioconductor-edger | 2017_03_29__10_51_56 | Differential expression analysis of rna-seq expression profiles with biological replication. implements a range of statistical methodology based on the negative binomial distributions, including empirical bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. as well as rna-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including chip-seq, sage and cage. | URL |
| 141 | bioconductor-fastseg | 2016_12_06__08_34_16 | Fastseg implements a very fast and efficient segmentation algorithm. it has similar functionality as dnacopy (olshen and venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from dna microarrays and data from next generation sequencing for example to detect copy number segments. further it can segment data from rna microarrays like tiling arrays to identify transcripts. most generally, it can segment data given as a matrix or as a vector. various data formats can be used as input to fastseg like expression set objects for microarrays or granges for sequencing data. the segmentation criterion of fastseg is based on a statistical test in a bayesian framework, namely the cyber t-test (baldi 2001). the speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments. | URL |
| 142 | bioconductor-flowai | 2016_09_06__16_56_56 | The package is able to perform an automatic or interactive quality control on fcs data acquired using flow cytometry instruments. by evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies. | URL |
| 143 | bioconductor-flowcl | 2017_03_17__15_09_11 | Semantic labelling of flow cytometric cell populations. | URL |
| 144 | bioconductor-flowcore | 2017_02_08__01_03_15 | Provides s4 data structures and basic functions to deal with flow cytometry data. | URL |
| 145 | bioconductor-flowdensity | 2017_02_08__07_50_24 | This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data. | URL |
| 146 | bioconductor-flowfp | 2017_02_12__03_56_19 | None | URL |
| 147 | bioconductor-flowviz | 2017_02_12__03_54_05 | None | URL |
| 148 | bioconductor-fourcseq | 2017_02_04__07_53_06 | Fourcseq is an r package dedicated to the analysis of (multiplexed) 4c sequencing data. the package provides a pipeline to detect specific interactions between dna elements and identify differential interactions between conditions. the statistical analysis in r starts with individual bam files for each sample as inputs. to obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. with a standard alignment software the required bam files can be then be generated. | URL |
| 149 | bioconductor-gage | 2016_05_03__23_07_11 | 'gage is a published method for gene set (enrichment or gsea) or pathway | URL |
| 150 | bioconductor-gagedata | 2016_10_08__12_08_36 | This is a supportive data package for the software package, gage. however, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. in this package, we provide two demo microarray dataset: gse16873 (a breast cancer dataset from geo) and bmp6 (originally published as an demo dataset for gage, also registered as gse13604 in geo). this package also includes commonly used gene set data based on kegg pathways and go terms for major research species, including human, mouse, rat and budding yeast. mapping data between common gene ids for budding yeast are also included. | URL |
| 151 | bioconductor-genebreak | 2017_01_22__11_34_39 | Recurrent breakpoint gene detection on copy number aberration profiles. | URL |
| 152 | bioconductor-genefilter | 2017_02_15__08_08_55 | Some basic functions for filtering genes | URL |
| 153 | bioconductor-genelendatabase | 2016_09_07__05_31_52 | Length of mrna transcripts for a number of genomes and gene id formats, largely based on ucsc table browser | URL |
| 154 | bioconductor-geneplotter | 2016_09_06__18_09_14 | Functions for plotting genomic data | URL |
| 155 | bioconductor-genomation | 2017_02_06__18_53_41 | A package for summary and annotation of genomic intervals. users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. the genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from ht-seq experiments, tf binding sites, methylation scores, etc. the package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. in addition, it can use bam or bigwig files as input. | URL |
| 156 | bioconductor-genomeinfodb | 2016_09_04__23_35_45 | Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. | URL |
| 157 | bioconductor-genomicalignments | 2016_11_04__07_08_36 | Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). this includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. | URL |
| 158 | bioconductor-genomicfeatures | 2016_11_04__07_12_21 | A set of tools and methods for making and manipulating transcript centric annotations. with these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the ucsc genome browser or a biomart database (more sources will be supported in the future). this information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. flexible methods are provided for extracting the desired features in a convenient format. | URL |
| 159 | bioconductor-genomicranges | 2016_11_03__13_45_06 | The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. ngs data). the genomicranges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. more specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the genomicalignments and summarizedexperiment packages respectively. both packages build on top of the genomicranges infrastructure. | URL |
| 160 | bioconductor-geoquery | 2016_10_08__17_05_15 | The ncbi gene expression omnibus (geo) is a public repository of microarray data. given the rich and varied nature of this resource, it is only natural to want to apply bioconductor tools to these data. geoquery is the bridge between geo and bioconductor. | URL |
| 161 | bioconductor-ggbio | 2016_11_04__23_35_56 | The ggbio package extends and specializes the grammar of graphics for biological data. the graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. all core bioconductor data structures are supported, where appropriate. the package supports detailed views of particular genomic regions, as well as genome-wide overviews. supported overviews include ideograms and grand linear views. high-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | URL |
| 162 | bioconductor-ggtree | 2016_10_29__07_07_51 | Ggtree extends the ggplot2 plotting system which implemented the grammar of graphics. ggtree is designed for visualizing phylogenetic tree and different types of associated annotation data. | URL |
| 163 | bioconductor-go.db | 2017_03_29__16_53_21 | A set of annotation maps describing the entire gene ontology assembled using data from go | URL |
| 164 | bioconductor-gosemsim | 2016_10_29__07_11_36 | Implemented five methods proposed by resnik, schlicker, jiang, lin and wang respectively for estimating go semantic similarities. support many species, including anopheles, arabidopsis, bovine, canine, chicken, chimp, coelicolor, e coli strain k12 and sakai, fly, gondii, human, malaria, mouse, pig, rhesus, rat, worm, xenopus, yeast, and zebrafish. | URL |
| 165 | bioconductor-goseq | 2017_03_29__16_54_57 | Detects gene ontology and/or other user defined categories which are over/under represented in rna-seq data | URL |
| 166 | bioconductor-gostats | 2016_10_29__07_16_45 | A set of tools for interacting with go and microarray data. a variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. | URL |
| 167 | bioconductor-gothic | 2017_01_05__16_52_25 | This is a hi-c analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in hi-c experiments. it takes mapped paired ngs reads as input and gives back the list of significant interactions for a given bin size in the genome. | URL |
| 168 | bioconductor-graph | 2016_10_25__22_53_47 | A package that implements some simple graph handling capabilities. | URL |
| 169 | bioconductor-graphite | 2016_10_07__07_08_09 | Graph objects from pathway topology derived from biocarta, humancyc, kegg, nci, panther, reactome and spike databases. | URL |
| 170 | bioconductor-gseabase | 2016_10_26__03_01_47 | This package provides classes and methods to support gene set enrichment analysis (gsea). | URL |
| 171 | bioconductor-gviz | 2016_11_07__22_48_30 | Genomic data analyses requires integrated visualization of known genomic information and new experimental data. gviz uses the biomart and the rtracklayer packages to perform live annotation queries to ensembl and ucsc and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. this results in genomic information plotted together with your data. | URL |
| 172 | bioconductor-heatplus | 2017_01_28__08_47_28 | Display a rectangular heatmap (intensity plot) of a data matrix. by default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. optionally, panels with additional information about samples and features can be added to the plot. | URL |
| 173 | bioconductor-hilbertvis | 2016_12_21__07_23_17 | Functions to visualize long vectors of integer data by means of hilbert curves | URL |
| 174 | bioconductor-hom.hs.inp.db | 2017_03_01__03_48_40 | None | URL |
| 175 | bioconductor-hpar | 2016_09_29__20_24_11 | A simple interface to and data from the human protein atlas project. | URL |
| 176 | bioconductor-ihw | 2016_12_21__07_25_54 | Independent hypothesis weighting (ihw) is a multiple testing procedure that increases power compared to the method of benjamini and hochberg by assigning data-driven weights to each hypothesis. the input to ihw is a two-column table of p-values and covariates. the covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis. | URL |
| 177 | bioconductor-illuminaio | 2016_10_08__17_17_21 | Tools for parsing illumina's microarray output files, including idat. | URL |
| 178 | bioconductor-illuminamousev2.db | 2016_09_06__22_05_06 | Illumina mousewg6v2 annotation data (chip illuminamousev2) assembled using data from public repositories | URL |
| 179 | bioconductor-impute | 2016_10_08__12_11_22 | Imputation for microarray data (currently knn only) | URL |
| 180 | bioconductor-iranges | 2016_11_03__13_48_03 | The package provides efficient low-level and highly reusable s4 classes for storing ranges of integers, rle vectors (run-length encoding), and, more generally, data that can be organized sequentially (formally defined as vector objects), as well as views on these vector objects. efficient list-like classes are also provided for storing big collections of instances of the basic classes. all classes in the package use consistent naming and share the same rich and consistent "vector api" as much as possible. | URL |
| 181 | bioconductor-isomirs | 2016_11_07__22_53_43 | Characterization of mirnas and isomirs, clustering and differential expression. | URL |
| 182 | bioconductor-jmosaics | 2016_09_08__00_20_47 | Jmosaics detects enriched regions of chip-seq data sets jointly. | URL |
| 183 | bioconductor-kcsmart | 2017_03_08__11_19_35 | None | URL |
| 184 | bioconductor-kegg.db | 2016_09_07__15_30_56 | A set of annotation maps for kegg assembled using data from kegg | URL |
| 185 | bioconductor-kegggraph | 2016_10_30__07_09_29 | Kegggraph is an interface between kegg pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. it parses the regularly updated kgml (kegg xml) files into graph models maintaining all essential pathway attributes. the package offers functionalities including parsing, graph operation, visualization and etc. | URL |
| 186 | bioconductor-keggrest | 2016_10_29__07_20_10 | A package that provides a client interface to the kegg rest server. based on keggsoap by j. zhang, r. gentleman, and marc carlson, and kegg (python package) by aurelien mazurie. | URL |
| 187 | bioconductor-limma | 2017_03_28__19_10_50 | Data analysis, linear models and differential expression for microarray data. | URL |
| 188 | bioconductor-lpsymphony | 2016_12_21__07_28_25 | This package was derived from rsymphony_0.1-17 from cran. these packages provide an r interface to symphony, an open-source linear programming solver written in c++. the main difference between this package and rsymphony is that it includes the solver source code (symphony version 5.6), while rsymphony expects to find header and library files on the users' system. thus the intention of lpsymphony is to provide an easy to install interface to symphony. for windows, precompiled dlls are included in this package. | URL |
| 189 | bioconductor-made4 | 2016_10_01__08_02_51 | Multivariate data analysis and graphical display of microarray data. functions include between group analysis and coinertia analysis. it contains functions that require ade4. | URL |
| 190 | bioconductor-marray | 2016_10_08__12_14_23 | Class definitions for two-color spotted microarray data. fuctions for data input, diagnostic plots, normalization and quality checking. | URL |
| 191 | bioconductor-masigpro | 2016_12_21__07_31_10 | Masigpro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and rna-seq experiments. | URL |
| 192 | bioconductor-massspecwavelet | 2017_03_22__14_36_48 | None | URL |
| 193 | bioconductor-medips | 2016_12_21__07_34_52 | Medips was developed for analyzing data derived from methylated dna immunoprecipitation (medip) experiments followed by sequencing (medip-seq). however, medips provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. chip-seq, mbd-seq, cms-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis. | URL |
| 194 | bioconductor-metagenomeseq | 2016_12_21__07_37_39 | Metagenomeseq is designed to determine features (be it operational taxanomic unit (otu), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeseq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. | URL |
| 195 | bioconductor-metams | 2016_10_31__07_11_03 | Ms-based metabolomics data processing and compound annotation pipeline. | URL |
| 196 | bioconductor-methylkit | 2017_03_11__10_22_07 | Methylkit is an r package for dna methylation analysis and annotation from high-throughput bisulfite sequencing. the package is designed to deal with sequencing data from rrbs and its variants, but also target-capture methods and whole genome bisulfite sequencing. it also has functions to analyze base-pair resolution 5hmc data from experimental protocols such as oxbs-seq and tab-seq. perl is needed to read sam files only. | URL |
| 197 | bioconductor-mgug4122a.db | 2016_09_07__01_15_07 | Agilent "mouse genome, whole" annotation data (chip mgug4122a) assembled using data from public repositories | URL |
| 198 | bioconductor-mmdiff | 2016_09_29__21_45_45 | This package detects statistically significant difference between read enrichment profiles in different chip-seq samples. to take advantage of shape differences it uses kernel methods (maximum mean discrepancy, mmd). | URL |
| 199 | bioconductor-mosaics | 2016_09_07__01_37_40 | This package provides functions for fitting mosaics and mosaics-hmm, a statistical framework to analyze one-sample or two-sample chip-seq data of transcription factor binding and histone modification. | URL |
| 200 | bioconductor-motifbreakr | 2017_02_03__13_06_20 | We introduce motifbreakr, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. motifbreakr is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. motifbreakr can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. lastly, it can be used to interrogate any genome curated within bioconductor (currently there are 22). | URL |
| 201 | bioconductor-motifdb | 2017_01_28__08_48_19 | More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms. | URL |
| 202 | bioconductor-motifrg | 2016_11_11__07_18_30 | Tools for discriminative motif discovery using regression methods | URL |
| 203 | bioconductor-motifstack | 2017_02_03__04_11_51 | The motifstack package is designed for graphic representation of multiple motifs with different similarity scores. it works with both dna/rna sequence motif and amino acid sequence motif. in addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors. | URL |
| 204 | bioconductor-motiv | 2017_01_31__14_58_19 | This package makes use of stamp for comparing a set of motifs to a given database (e.g. jaspar). it can also be used to visualize motifs, motif distributions, modules and filter motifs. | URL |
| 205 | bioconductor-multtest | 2016_10_08__20_39_20 | Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical bayes methods) for controlling the family-wise error rate (fwer), generalized family-wise error rate (gfwer), tail probability of the proportion of false positives (tppfp), and false discovery rate (fdr). several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). single-step and step-wise methods are available. tests based on a variety of t- and f-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. when probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. the procedures are directly applicable to identifying differentially expressed genes in dna microarray experiments. | URL |
| 206 | bioconductor-mzr | 2017_01_26__06_18_19 | Mzr provides a unified api to the common file formats and parsers available for mass spectrometry data. it comes with a wrapper for the isb random access parser for mass spectrometry mzxml, mzdata and mzml files. the package contains the original code written by the isb, and a subset of the proteowizard library for mzml and mzidentml. the netcdf reading code has previously been used in xcms. | URL |
| 207 | bioconductor-noiseq | 2016_11_21__06_48_59 | Analysis of rna-seq expression data or other similar kind of data. exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. differential expression between two experimental conditions with no parametric assumptions. | URL |
| 208 | bioconductor-org.ce.eg.db | 2016_09_29__23_13_52 | Genome wide annotation for worm, primarily based on mapping using entrez gene identifiers. | URL |
| 209 | bioconductor-org.dm.eg.db | 2017_03_23__15_08_55 | Genome wide annotation for fly, primarily based on mapping using entrez gene identifiers. | URL |
| 210 | bioconductor-org.hs.eg.db | 2016_10_08__17_30_22 | Genome wide annotation for human, primarily based on mapping using entrez gene identifiers. | URL |
| 211 | bioconductor-org.mm.eg.db | 2017_03_23__15_10_31 | Genome wide annotation for mouse, primarily based on mapping using entrez gene identifiers. | URL |
| 212 | bioconductor-organismdbi | 2016_09_06__00_05_16 | The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods. | URL |
| 213 | bioconductor-pathview | 2017_01_28__07_46_15 | 'pathview is a tool set for pathway based data integration and visualization. | URL |
| 214 | bioconductor-pcaexplorer | 2017_03_31__00_07_04 | None | URL |
| 215 | bioconductor-pcamethods | 2016_09_06__00_53_43 | Provides bayesian pca, probabilistic pca, nipals pca, inverse non-linear pca and the conventional svd pca. a cluster based method for missing value estimation is included for comparison. bpca, ppca and nipalspca may be used to perform pca on incomplete data as well as for accurate missing value estimation. a set of methods for printing and plotting the results is also provided. all pca methods make use of the same data structure (pcares) to provide a common interface to the pca results. initiated at the max-planck institute for molecular plant physiology, golm, germany. | URL |
| 216 | bioconductor-pchicdata | 2017_01_11__16_16_13 | Subsets of promoter capture hi-c data conveniently packaged for chicago users. data includes interactions detected for chromosomes 20 and 21 in gm12878 cells and for chromosomes 18 and 19 in mesc. | URL |
| 217 | bioconductor-phyloseq | 2017_02_05__08_30_17 | Phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. | URL |
| 218 | bioconductor-piano | 2016_10_06__21_57_47 | Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. furthermore, the piano package contains functions for combining the results of multiple runs of gene set analyses. | URL |
| 219 | bioconductor-preprocesscore | 2016_10_08__17_49_09 | A library of core preprocessing routines | URL |
| 220 | bioconductor-probamr | 2017_01_26__10_14_56 | Mapping psms back to genome. the package builds sam file from shotgun proteomics data the package also provides function to prepare annotation from gtf file. | URL |
| 221 | bioconductor-protgenerics | 2016_10_08__12_17_07 | S4 generic functions needed by bioconductor proteomics packages. | URL |
| 222 | bioconductor-qdnaseq | 2016_12_06__21_35_25 | Quantitative dna sequencing for chromosomal aberrations. the genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and gc content, and filtered to remove spurious regions in the genome. downstream steps of segmentation and calling are also implemented via packages dnacopy and cghcall, respectively. | URL |
| 223 | bioconductor-qdnaseq.mm10 | 2017_01_21__07_48_30 | This package provides qdnaseq bin annotations for the mouse genome build mm10. | URL |
| 224 | bioconductor-qvalue | 2017_03_29__16_50_24 | This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local fdr values. the q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. the local fdr measures the posterior probability the null hypothesis is true given the test's p-value. various plots are automatically generated, allowing one to make sensible significance cut-offs. several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. the software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. | URL |
| 225 | bioconductor-rbgl | 2016_10_08__17_52_12 | A fairly extensive and comprehensive interface to the graph algorithms contained in the boost library. | URL |
| 226 | bioconductor-rcas | 2017_03_23__13_23_16 | Rna centric annotation system (rcas) is an automated system that provides dynamic annotations for custom input files that contain transcriptomic targe regions. | URL |
| 227 | bioconductor-rcytoscape | 2016_09_29__18_21_01 | Interactvive viewing and exploration of graphs, connecting r to cytoscape. | URL |
| 228 | bioconductor-regioner | 2017_02_05__07_27_29 | Regioner offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features. | URL |
| 229 | bioconductor-repitools | 2016_11_25__15_58_13 | Tools for the analysis of enrichment-based epigenomic data. features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, baymeth for quantifying methylation etc. | URL |
| 230 | bioconductor-rgadem | 2017_01_28__18_18_42 | Rgadem is an efficient de novo motif discovery tool for large-scale genomic sequence data. it is an open-source r package, which is based on the gadem software. | URL |
| 231 | bioconductor-rgalaxy | 2017_01_28__21_46_13 | Given an r function and its manual page, make the documented function available in galaxy. | URL |
| 232 | bioconductor-rgraphviz | 2017_01_28__02_11_21 | 'interfaces r with the at and t graphviz library for plotting r graph objects | URL |
| 233 | bioconductor-rhdf5 | 2017_02_03__04_09_32 | This r/bioconductor package provides an interface between hdf5 and r. hdf5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. the rhdf5 package is thus suited for the exchange of large and/or complex datasets between r and other software package, and for letting r applications work on datasets that are larger than the available ram. | URL |
| 234 | bioconductor-rhtslib | 2017_01_27__07_41_42 | This package provides version 1.1 of the "htslib" c library for high-throughput sequence analysis. the package is primarily useful to developers of other r packages who wish to make use of htslib. motivation and instructions for use of this package are in the vignette, vignette(package="rhtslib", "rhtslib"). | URL |
| 235 | bioconductor-ringo | 2016_11_25__15_46_21 | The package ringo facilitates the primary analysis of chip-chip data. the main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in chip-chip. the package has functions to deal with two-color oligonucleotide microarrays from nimblegen used in chip-chip projects, but also contains more general functions for chip-chip data analysis, given that the data is supplied as rglist (raw) or expressionset (pre- processed). the package employs functions from various other packages of the bioconductor project and provides additional chip-chip-specific and nimblegen-specific functionalities. | URL |
| 236 | bioconductor-rnaseqpower | 2016_10_28__07_06_41 | Rna-seq, sample size | URL |
| 237 | bioconductor-roar | 2017_02_05__19_43_53 | None | URL |
| 238 | bioconductor-ropls | 2016_10_08__17_55_06 | Latent variable modeling with principal component analysis (pca) and partial least squares (pls) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. orthogonal partial least squares (opls) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. while performing similarly to pls, opls facilitates interpretation. successful applications of these chemometrics techniques include spectroscopic data such as raman spectroscopy, nuclear magnetic resonance (nmr), mass spectrometry (ms) in metabolomics and proteomics, but also transcriptomics data. in addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the r2 and q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with variable importance in projection or regression coefficients). the package can be accessed via a user interface on the workflow4metabolomics.org online resource for computational metabolomics (built upon the galaxy environment). | URL |
| 239 | bioconductor-rsamtools | 2016_11_03__13_51_20 | This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'licence') for manipulating sam (sequence alignment / map), fasta, binary variant call (bcf) and compressed indexed tab-delimited (tabix) files. | URL |
| 240 | bioconductor-rsubread | 2017_03_27__08_46_57 | Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and snp calling. can be used with reads generated from any of the major sequencing platforms including illumina ga/hiseq/miseq, roche gs-flx, abi solid and lifetech ion pgm/proton sequencers. | URL |
| 241 | bioconductor-rtracklayer | 2016_11_04__07_16_10 | Extensible framework for interacting with multiple genome browsers (currently ucsc built-in) and manipulating annotation tracks in various formats (currently gff, bed, bedgraph, bed15, wig, bigwig and 2bit built-in). the user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport. | URL |
| 242 | bioconductor-s4vectors | 2016_11_03__13_54_02 | The s4vectors package defines the vector and list virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in r. package developers can easily implement vector-like or list-like objects as concrete subclasses of vector or list. in addition, a few low-level concrete subclasses of general interest (e.g. dataframe, rle, and hits) are implemented in the s4vectors package itself (many more are implemented in the iranges package and in other bioconductor infrastructure packages). | URL |
| 243 | bioconductor-seqlogo | 2016_10_08__12_20_40 | Seqlogo takes the position weight matrix of a dna sequence motif and plots the corresponding sequence logo as introduced by schneider and stephens (1990). | URL |
| 244 | bioconductor-seqpattern | 2016_11_11__07_21_43 | Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature. | URL |
| 245 | bioconductor-shortread | 2016_12_06__21_36_30 | This package implements sampling, iteration, and input of fastq files. the package includes functions for filtering and trimming reads, and for generating a quality assessment report. data are represented as dnastringset-derived objects, and easily manipulated for a diversity of purposes. the package also contains legacy support for early single-end, ungapped alignment formats. | URL |
| 246 | bioconductor-siggenes | 2016_09_30__13_14_13 | Identification of differentially expressed genes and estimation of the false discovery rate (fdr) using both the significance analysis of microarrays (sam) and the empirical bayes analyses of microarrays (ebam). | URL |
| 247 | bioconductor-sradb | 2017_02_05__07_26_40 | The sequence read archive (sra) is the largest public repository of sequencing data from the next generation of sequencing platforms including roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, and others. however, finding data of interest can be challenging using current tools. sradb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. this is accomplished by parsing all the ncbi sra metadata into a sqlite database that can be stored and queried locally. fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. beside ftp protocol, the sradb has funcitons supporting fastp protocol (ascp from aspera connect) for faster downloading large data files over long distance. the sqlite database is updated regularly as new data is added to sra and can be downloaded at will for the most up-to-date metadata. | URL |
| 248 | bioconductor-summarizedexperiment | 2016_11_03__13_57_03 | The summarizedexperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. the rows typically represent genomic ranges of interest and the columns represent samples. | URL |
| 249 | bioconductor-sva | 2016_09_06__08_57_14 | The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/rna sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. the sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (leek and storey 2007 plos genetics,2008 pnas), (2) directly removing known batch effects using combat (johnson et al. 2007 biostatistics) and (3) removing batch effects with known control probes (leek 2014 biorxiv). removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (leek and storey 2007 plos genetics, 2008 pnas or leek et al. 2011 nat. reviews genetics). | URL |
| 250 | bioconductor-synergyfinder | 2017_04_05__01_15_30 | None | URL |
| 251 | bioconductor-systempiper | 2016_09_08__07_55_05 | R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (ngs) applications such as rna-seq, chip-seq, var-seq and ribo-seq. important features include a uniform workflow interface across different ngs applications, automated report generation, and support for running both r and command-line software, such as ngs aligners or peak/variant callers, on local computers or compute clusters. efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. instructions for using systempiper are given in the overview vignette (html). the remaining vignettes, linked below, are workflow templates for common ngs use cases. | URL |
| 252 | bioconductor-topgo | 2016_10_20__07_08_10 | Topgo package provides tools for testing go terms while accounting for the topology of the go graph. different test statistics and different methods for eliminating local similarities and dependencies between go terms can be implemented and applied. | URL |
| 253 | bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene | 2016_09_07__03_04_54 | Exposes an annotation databases generated from ucsc by exposing these as txdb objects | URL |
| 254 | bioconductor-txdb.hsapiens.ucsc.hg19.knowngene | 2016_09_06__21_21_58 | Exposes an annotation databases generated from ucsc by exposing these as txdb objects | URL |
| 255 | bioconductor-txdb.mmusculus.ucsc.mm10.ensgene | 2016_11_02__20_22_38 | Exposes an annotation databases generated from ucsc by exposing these as txdb objects | URL |
| 256 | bioconductor-tximport | 2016_09_04__11_40_11 | Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts. | URL |
| 257 | bioconductor-variantannotation | 2016_09_06__10_26_16 | Annotate variants, compute amino acid coding changes, predict coding outcomes. | URL |
| 258 | bioconductor-vsn | 2016_09_06__21_36_10 | Data analysis, linear models and differential expression for microarray data. | URL |
| 259 | bioconductor-xcms | 2017_03_22__15_11_32 | Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. imports from aia/andi netcdf, mzxml, mzdata and mzml files. preprocesses data for high-throughput, untargeted analyte profiling. | URL |
| 260 | bioconductor-xvector | 2016_10_03__07_07_07 | Memory efficient s4 classes for storing sequences "externally" (behind an r external pointer, or on disk). | URL |
| 261 | bioconductor-zlibbioc | 2017_03_09__04_53_24 | This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most linux and mac users should have system-level access to zlib, and no direct need for this package). see the vignette for instructions on use. | URL |
| 262 | bioepic | 2016_09_05__13_34_33 | None | URL |
| 263 | biogridpy | 2016_10_17__21_14_31 | Python client for the biogrid rest api webservice | URL |
| 264 | biokit | 2017_03_02__11_03_05 | Access to biological web services from python | URL |
| 265 | biom-format | 2016_05_10__12_59_23 | Biological observation matrix (biom) format | URL |
| 266 | biomaj | 2016_10_25__07_06_06 | Automates the update cycle and the supervision of the locally mirrored databank repository | URL |
| 267 | biopython | 2016_09_14__07_08_26 | Freely available tools for computational molecular biology. | URL |
| 268 | bioservices | 2017_02_14__12_35_44 | Access to biological web services from python | URL |
| 269 | bismark | 2017_01_26__08_38_11 | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. the output can be easily imported into a genome viewer, such as seqmonk, and enables a researcher to analyse the methylation levels of their samples straight away. | URL |
| 270 | bitstring | 2016_09_06__14_27_33 | Simple construction, analysis and modification of binary data. | URL |
| 271 | blasr | 2017_03_28__19_10_42 | blasr - the pacbio long read aligner | URL |
| 272 | blasr_libcpp | 2017_02_18__16_10_39 | blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadpulses for analyzing pacbio sequences | URL |
| 273 | blast | 2017_02_19__16_38_31 | Blast+ is a new suite of blast tools that utilizes the ncbi c++ toolkit. | URL |
| 274 | blast-legacy | 2016_09_05__09_30_27 | The basic local alignment search tool (blast) finds regions of local similarity between sequences. | URL |
| 275 | blastalign | 2017_03_02__08_00_20 | None | URL |
| 276 | blat | 2016_09_06__13_58_28 | Blat is a bioinformatics software tool which performs rapid mrna/dna and cross-species protein alignments. | URL |
| 277 | bleach | 2016_09_07__20_02_09 | An easy whitelist-based html-sanitizing tool. | URL |
| 278 | blinker | 2016_09_08__01_28_54 | Fast, simple object-to-object and broadcast signaling | URL |
| 279 | blockbuster | 2016_09_04__22_08_13 | Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. | URL |
| 280 | bmtagger | 2016_09_05__10_25_56 | Bmtagger aka best match tagger is for removing human reads from metagenomics datasets | URL |
| 281 | bmtool | 2017_04_11__17_59_35 | Bmtool is part of bmtagger aka best match tagger, for removing human reads from metagenomics datasets | URL |
| 282 | boltons | 2016_09_07__18_21_27 | None | URL |
| 283 | botocore | 2016_09_08__01_17_53 | None | URL |
| 284 | bottle | 2016_09_08__01_00_34 | Fast and simple wsgi-framework for small web-applications. | URL |
| 285 | boutroslabplottinggeneral | 2017_02_06__00_54_32 | None | URL |
| 286 | bowtie | 2017_01_08__07_35_03 | An ultrafast memory-efficient short read aligner | URL |
| 287 | bowtie2 | 2017_01_28__23_36_21 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. it is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. bowtie 2 indexes the genome with an fm index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gb. bowtie 2 supports gapped, local, and paired-end alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | URL |
| 288 | bpipe | 2017_03_15__08_06_54 | None | URL |
| 289 | braker | 2016_09_05__13_54_48 | Braker1: unsupervised rna-seq-based genome annotation with genemark-et and augustus | URL |
| 290 | brass | 2016_12_03__08_57_13 | None | URL |
| 291 | breakdancer | 2017_02_25__09_35_59 | None | URL |
| 292 | breseq | 2017_01_30__07_44_10 | 'a computational pipeline for finding mutations relative to a reference sequence in short-read dna re-sequencing data.' | URL |
| 293 | brewer2mpl | 2016_09_07__21_37_50 | Connect colorbrewer2.org color maps to python and matplotlib | URL |
| 294 | bs-seeker2 | 2017_01_26__08_37_42 | Bs seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads. | URL |
| 295 | bumbershoot | 2016_12_16__07_19_30 | the bumbershoot tool suite for analyzing shotgun proteomic data | URL |
| 296 | burrito | 2016_09_08__10_13_27 | Framework for wrapping and controlling command-line applications. | URL |
| 297 | busco | 2017_01_09__15_11_48 | Busco provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from orthodb. | URL |
| 298 | bwa | 2016_11_16__08_47_33 | The bwa read mapper. | URL |
| 299 | bwameth | 2016_09_14__15_45_39 | A fast and accurate aligner of bs-seq reads | URL |
| 300 | bx-python | 2016_09_09__04_12_33 | Toolkit to enable rapid implementation of genome scale analyses. | URL |
| 301 | byobu | 2017_04_11__17_59_35 | Byobu is a gplv3 open source text-based window manager and terminal multiplexer. | URL |
| 302 | cage | 2016_09_05__02_20_50 | Changepoint analysis for efficient variant calling | URL |
| 303 | cancerit-allelecount | 2016_05_08__11_59_30 | Support code for ngs copy number algorithms | URL |
| 304 | cansam | 2016_09_20__13_01_09 | None | URL |
| 305 | canu | 2017_01_09__01_03_19 | Canu is a fork of the celera assembler designed for high-noise single-molecule sequencing. | URL |
| 306 | canvas | 2017_04_03__08_17_55 | None | URL |
| 307 | carna | 2017_01_22__23_36_53 | Constraint-based alignment of rna ensembles | URL |
| 308 | ccat | 2016_05_08__11_59_50 | ccat is a software package for the analysis of chip-seq data with negative control. | URL |
| 309 | cd-hit | 2016_09_18__10_31_49 | clusters and compares protein or nucleotide sequences | URL |
| 310 | cdbtools | 2016_05_08__12_00_15 | Cdb (constant database) indexing and retrieval tools for fasta files | URL |
| 311 | ceas | 2016_05_08__12_00_55 | Ceas: cis-regulatory element annotation system | URL |
| 312 | centrifuge | 2017_01_16__08_27_51 | 'classifier for metagenomic sequences.' | URL |
| 313 | cgat-pipelines-nosetests | 2017_03_09__18_18_42 | Metapackage to test cgat pipelines | URL |
| 314 | cgat-report | 2017_04_03__12_18_03 | None | URL |
| 315 | cgat-scripts-devel | 2017_01_30__09_50_18 | Computational genomics analysis toolkit | URL |
| 316 | cgat-scripts-nosetests | 2017_01_19__18_56_11 | Computational genomics analysis toolkit | URL |
| 317 | cgcloud-lib | 2017_02_10__13_25_50 | Components shared between cgcloud-core and cgcloud-agent | URL |
| 318 | chainmap | 2016_09_08__03_04_35 | Backport/clone of chainmap for py26, py32, and pypy3. | URL |
| 319 | chanjo | 2016_05_08__12_01_55 | Coverage analysis tool for clinical sequencing | URL |
| 320 | check-sort-order | 2016_09_05__10_51_03 | Check sort-order of genomic files according to a genomefile | URL |
| 321 | checkm-genome | 2016_09_09__07_36_13 | Assess the quality of putative genome bins. | URL |
| 322 | chemfp | 2016_05_16__18_03_40 | Chemfp is a set of command-lines tools for generating cheminformatics\nfingerprints and searching those fingerprints by tanimoto similarity,\nas well as a python library which can be used to build new tools.\n\nthese algorithms are designed for the dense, 100-10,000 bit\nfingerprints which occur in small-molecule/pharmaceutical\nchemisty. the tanimoto search algorithms are implemented in c for\nperformance and support both threshold and k-nearest searches.\n\nfingerprint generation can be done either by extracting existing\nfingerprint data from an sd file or by using an existing chemistry\ntoolkit. chemfp supports the python libraries from open babel,\nopeneye, and rdkit toolkits.\n | URL |
| 323 | chicagotools | 2017_01_25__07_54_05 | None | URL |
| 324 | chromhmm | 2017_03_17__19_12_07 | Chromhmm is software for learning and characterizing chromatin states. chromhmm can integrate multiple chromatin datasets such as chip-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. | URL |
| 325 | circexplorer | 2016_09_07__17_11_00 | A combined strategy to identify circular rnas (circrnas and cirnas) | URL |
| 326 | circexplorer2 | 2016_10_03__06_32_28 | Circular rna analysis toolkits | URL |
| 327 | circlator | 2017_04_03__16_48_58 | Circlator: a tool to circularise genome assemblies | URL |
| 328 | circos | 2017_02_27__14_01_17 | Circos is a software package for visualizing data and information. it visualizes data in a circular layout | URL |
| 329 | cityhash | 2016_11_17__17_43_39 | Python-bindings for cityhash, a fast non-cryptographic hash algorithm | URL |
| 330 | clark | 2016_12_24__07_22_56 | Fast, accurate and versatile k-mer based classification system | URL |
| 331 | clearcut | 2016_09_05__10_59_43 | The reference implementation for relaxed neighbor joining (rnj). | URL |
| 332 | clever-toolkit | 2017_03_22__16_26_35 | The clever toolkit (ctk) is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads. | URL |
| 333 | click | 2016_09_07__14_27_44 | A simple wrapper around optparse for powerful command line utilities. | URL |
| 334 | cluster-picker | 2017_01_25__07_39_48 | The cluster picker identifies clusters in newick-formatted trees containing thousands of sequences within a few minutes. cut-offs for within cluster genetic distance and bootstrap support are selected by the user. | URL |
| 335 | cmfinder | 2017_03_17__21_27_32 | Cmfinder - a covariance model based rna motif finding algorithm | URL |
| 336 | cmph | 2017_03_04__16_27_36 | None | URL |
| 337 | cnvkit | 2017_03_05__14_35_02 | Copy number variant detection from targeted dna sequencing | URL |
| 338 | cobra | 2016_05_08__15_33_12 | Cobrapy is a package for constraint-based modeling of biological networks | URL |
| 339 | cofold | 2016_07_28__19_23_46 | An rna secondary structure prediction method that takes co-transcriptional folding into account. | URL |
| 340 | cogent | 2016_09_09__07_54_17 | Comparative genomics toolkit | URL |
| 341 | colorbrewer | 2016_09_07__14_24_25 | An easy way to get access to colorbrewer schemes from within a python program | URL |
| 342 | colormap | 2016_09_05__04_09_03 | Utilities to ease manipulation of matplotlib colormaps and color codecs (e.g., hex2rgb) | URL |
| 343 | concoct | 2017_02_13__07_54_09 | None | URL |
| 344 | coreutils | 2016_09_06__10_18_52 | The gnu core utilities are the basic file, shell and text manipulation utilities of the gnu operating system. these are the core utilities which are expected to exist on every operating system. | URL |
| 345 | cosi2 | 2016_09_05__11_18_29 | Cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. it supports exact and approximate simulation modes. | URL |
| 346 | cpat | 2016_09_08__04_56_08 | Coding potential assessment tool | URL |
| 347 | cramtools | 2016_09_05__11_35_22 | A set of java tools and apis for efficient compression of sequence read data | URL |
| 348 | crb-blast | 2016_09_05__11_45_10 | Conditional reciprocal best blast - high confidence ortholog assignment. | URL |
| 349 | crispresso | 2016_09_21__07_30_52 | A software pipeline for the analysis of targeted crispr-cas9 sequencing data | URL |
| 350 | cromwell | 2017_03_26__13_54_10 | A workflow management system geared towards scientific workflows described in wdl | URL |
| 351 | crossmap | 2016_05_08__15_38_41 | Convert genomic coordiates between assemblies | URL |
| 352 | csvtk | 2017_04_11__16_59_27 | A cross-platform, efficient, practical and pretty csv/tsv toolkit | URL |
| 353 | cufflinks | 2016_09_05__11_56_05 | Transcriptome assembly and differential expression analysis for rna-seq. | URL |
| 354 | curl | 2016_10_25__22_54_36 | Curl is an open source command line tool and library for transferring data with url syntax | URL |
| 355 | cutadapt | 2017_03_16__21_41_49 | Trim adapters from high-throughput sequencing reads | URL |
| 356 | cwl2wdl | 2017_03_29__14_40_06 | Proof of concept converter from common workflow language (cwl) to the broad institute's workflow definition language (wdl). | URL |
| 357 | cwltest | 2017_02_21__12_50_02 | Framework for testing cwl tools and workflows | URL |
| 358 | cwltool | 2017_03_28__10_24_28 | Common workflow language reference implementation | URL |
| 359 | cyordereddict | 2016_09_07__16_32_22 | Cython implementation of python's collections.ordereddict | URL |
| 360 | cyvcf2 | 2017_03_16__20_14_54 | A cython wrapper around htslib built for fast parsing of variant call format (vcf) files | URL |
| 361 | daligner | 2017_02_07__05_44_43 | Daligner: find all significant local alignments between reads | URL |
| 362 | damidseq_pipeline | 2017_03_28__08_17_04 | None | URL |
| 363 | dammit | 2017_04_11__17_59_35 | Simple de novo transcriptome annotation | URL |
| 364 | data_hacks | 2016_09_07__16_37_56 | Command line utilities for data analysis. | URL |
| 365 | datamash | 2016_09_05__12_19_03 | Gnu datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files. | URL |
| 366 | dazz_db | 2017_01_26__10_13_46 | Dazz_db: the dazzler data base | URL |
| 367 | dcmtk | 2017_03_20__12_41_40 | "dcmtk is a collection of libraries and applications implementing large parts the dicom standard" | URL |
| 368 | ddocent | 2017_03_30__19_01_19 | ddocent is an interactive bash wrapper to qc, assemble, map, and call snps from double digest rad data | URL |
| 369 | ddrage | 2017_03_18__21_43_01 | None | URL |
| 370 | deap | 2016_09_05__05_14_38 | Distributed evolutionary algorithms in python | URL |
| 371 | debwt | 2016_09_07__20_48_09 | A efficient method to construct bwt index of a given dna sequence, especially useful for gigantic and high similar genome. debwt has good scalability to construct bwt in parallel computing. it is well-suited to run on multiple core servers or clusters to construct the bwt of large collections of genome sequences. | URL |
| 372 | deepmedic | 2017_02_09__22_47_43 | None | URL |
| 373 | deeptools | 2017_03_31__11_37_59 | A set of user-friendly tools for normalization and visualzation of deep-sequencing data | URL |
| 374 | delly | 2016_10_25__22_55_19 | Structural variant discovery by integrated paired-end and split-read analysis | URL |
| 375 | dendropy | 2016_12_15__07_34_25 | A python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | URL |
| 376 | denovogear | 2016_09_05__12_43_44 | A program to detect denovo-variants using next-generation sequencing data. | URL |
| 377 | detonate | 2016_09_06__04_38_58 | Detonate (de novo transcriptome rna-seq assembly with or without the truth evaluation) consists of two component packages, rsem-eval and ref-eval. | URL |
| 378 | dextractor | 2016_09_25__13_14_35 | Bax file decoder and data compressor | URL |
| 379 | dfam | 2017_04_11__17_59_35 | The dfam database is a collection of repetitive dna element sequence alignments, hidden markov models (hmms) and matches lists for complete eukaryote genomes | URL |
| 380 | dia_umpire | 2016_09_28__14_51_27 | Dia-umpire is an open source java program for computational analysis of data independent acquisition (dia) mass spectrometry-based proteomics data. it enables untargeted peptide and protein identification and quantitation using dia data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation. | URL |
| 381 | diamond | 2017_02_19__09_54_35 | Accelerated blast compatible local sequence aligner | URL |
| 382 | disco | 2017_03_17__10_58_54 | None | URL |
| 383 | discovar | 2016_09_06__14_46_43 | Suitable for variant calling with reference and de novo assembly of small genomes. | URL |
| 384 | discovardenovo | 2016_09_08__09_06_17 | None | URL |
| 385 | dkfz-bias-filter | 2017_02_18__12_08_07 | The dkfz bias filter flags snvs that appear to be biased based on the variant read support | URL |
| 386 | dlcpar | 2016_12_22__07_39_22 | Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy! | URL |
| 387 | dnapi | 2017_03_23__18_31_09 | De novo adapter prediction (iterative) algorithm for small rna sequencing data. | URL |
| 388 | doit | 2016_09_05__12_47_23 | Doit - automation tool | URL |
| 389 | dr-disco | 2017_03_02__16_07_10 | Dr. disco: fusion gene breakpoint detection in total rna-seq data | URL |
| 390 | drive | 2017_02_03__04_12_06 | google drive client for the commandline | URL |
| 391 | dropbox | 2016_09_06__23_31_27 | Official dropbox api client | URL |
| 392 | dscr | 2016_10_26__08_38_27 | None | URL |
| 393 | dsrc | 2017_02_25__18_39_30 | High-performance compression of sequencing reads stored in fastq format | URL |
| 394 | dudes | 2016_11_23__23_04_22 | Dudes is a taxonomic profiler for ngs metagenomic samples | URL |
| 395 | dunovo | 2017_02_24__06_45_26 | None | URL |
| 396 | dwgsim | 2016_09_06__14_50_15 | Whole genome simulator for next-generation sequencing | URL |
| 397 | dxua | 2016_09_05__13_03_55 | Command-line tool for uploading files to the dnanexus platform | URL |
| 398 | e-pcr | 2016_09_05__13_16_00 | E-pcr identifies sequence tagged sites(stss)within dna sequences.. | URL |
| 399 | ea-utils | 2017_04_11__17_59_35 | Command-line tools for processing biological sequencing data. | URL |
| 400 | eagle | 2016_12_06__07_24_29 | Eagle is a webtool for genome variants and snp analysis | URL |
| 401 | easydev | 2017_02_08__12_49_11 | Common utilities to ease the development of python packages | URL |
| 402 | ecmwfapi | 2017_01_17__08_41_56 | Ecmwf api is a set of services developed by ecmwf http://www.ecmwf.int to allow users from the outside to access some internal features and data of the centre. | URL |
| 403 | ecopcr | 2016_12_03__08_12_27 | ecopcr is an electronic pcr software that helps you estimate barcode primers quality. | URL |
| 404 | ecoprimers | 2016_12_03__08_05_42 | ecoprimers is a software that finds primers from a set of sequence. | URL |
| 405 | eden | 2016_11_27__19_47_31 | The explicit decomposition with neighborhoods (eden) is a decompositional kernel based on the neighborhood subgraph pairwise distance kernel (nspdk) that can be used to induce an explicit feature representation for graphs. this in turn allows the adoption of machine learning algorithm to perform supervised and unsupervised learning task in a scalable way (e.g. using fast stochastic gradient descent methods in classification and approximate neighborhood queries in clustering). | URL |
| 406 | editdistance | 2017_04_03__08_19_19 | None | URL |
| 407 | edittag | 2016_12_05__08_24_40 | Design and check sets of edit metric sequence tags. | URL |
| 408 | edlib | 2017_02_20__04_58_31 | C/c++ library and program for sequence alignment using edit (levenshtein) distance | URL |
| 409 | eigen | 2017_04_11__17_59_35 | Eigen is a c++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | URL |
| 410 | eigensoft | 2017_04_11__17_59_35 | Population genetics - principal components analysis (pca) | URL |
| 411 | elasticluster | 2016_09_08__05_02_41 | Create, manage and setup computing clusters hosted on a public or private cloud infrastructure. | URL |
| 412 | emboss | 2016_09_24__21_19_55 | The european molecular biology open software suite | URL |
| 413 | emirge | 2016_12_07__07_17_16 | 'emirge reconstructs full length sequences from short sequencing reads' | URL |
| 414 | emmix | 2017_01_15__07_41_31 | A tool that fits a mixture model of multivariate normal or t-distributed components to a given data set. | URL |
| 415 | ensembl-vep | 2017_04_04__08_24_41 | None | URL |
| 416 | entrez-direct | 2016_09_05__13_08_40 | Entrez direct (edirect) is an advanced method for accessing the ncbi's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a unix terminal window. functions take search terms from command-line arguments. individual operations are combined to build multi-step queries. record retrieval and formatting normally complete the process. | URL |
| 417 | eoulsan | 2016_05_23__13_17_28 | A pipeline and a framework for ngs analysis (rna-seq and chip-seq) | URL |
| 418 | epic | 2017_01_18__13_03_06 | Chip-seq broad peak/domain finder. | URL |
| 419 | epydoc | 2016_09_07__23_34_59 | Edward loper's api documentation generation tool | URL |
| 420 | ericscript | 2017_03_10__11_55_02 | Ericscript is a computational framework for the discovery of gene fusions in paired end rna-seq data. it is able to generate synthetic gene fusions by using the ericscript simulator and calculate a number of statistical measures for evaluating gene fusion detection methods performance with ericscript calcstats. | URL |
| 421 | erne | 2017_03_03__08_02_02 | None | URL |
| 422 | esmre | 2016_09_06__23_11_38 | Regular expression accelerator | URL |
| 423 | estmapper | 2017_01_11__07_34_51 | "software package for the high-throughput alignment of large cdna (est, mrna) sequence sets to a large eukaryotic genome of the same species" | URL |
| 424 | estscan | 2016_12_09__07_16_45 | Detects coding regions in dna sequences even if they are of low quality | URL |
| 425 | eta | 2017_04_03__08_20_55 | None | URL |
| 426 | ete2 | 2017_01_08__07_42_40 | Phylogenetic tree analyses and exploration | URL |
| 427 | ete3 | 2017_04_05__08_23_28 | None | URL |
| 428 | exonerate | 2016_09_05__13_26_13 | exonerate - a generic tool for pairwise sequence comparison / alignment | URL |
| 429 | expansionhunter | 2017_03_31__19_27_11 | None | URL |
| 430 | exparna | 2016_11_03__13_59_33 | The program finds the longest common subsequence of exact pattern matches (lcs-epm) | URL |
| 431 | expat | 2016_09_06__21_20_21 | Expat is an xml parser library written in c. it is a stream-oriented parser in which an application registers handlers for things the parser might find in the xml document (like start tags). | URL |
| 432 | export2graphlan | 2016_09_05__13_49_58 | Export2graphlan is a conversion software tool for producing both annotation and tree file for graphlan | URL |
| 433 | express | 2017_04_11__17_59_35 | Express is a streaming dna/rna sequence quantification tool. | URL |
| 434 | extern | 2017_04_08__08_19_25 | None | URL |
| 435 | extract-sv-reads | 2017_01_19__10_35_54 | Tool for extracting splitter or discordant reads from a bam or cram file. | URL |
| 436 | extract_fullseq | 2016_11_02__20_32_44 | Extract_fullseq is part of bmtagger aka best match tagger, for removing human reads from metagenomics datasets | URL |
| 437 | fadapa | 2016_09_07__22_45_59 | Fastqc data parser - a minimal parser to parse fastqc output data | URL |
| 438 | fann | 2017_01_02__07_27_43 | Fast artificial neural network library | URL |
| 439 | fast5 | 2017_04_01__20_36_30 | 'a c++ header-only library for reading oxford nanopore fast5 files.' | URL |
| 440 | fasta3 | 2016_09_07__09_41_04 | The fasta package - protein and dna sequence similarity searching and alignment programs | URL |
| 441 | fastahack | 2017_04_04__08_31_38 | None | URL |
| 442 | fastaindex | 2017_01_19__15_24_19 | Fasta indexing and sequence retrival. | URL |
| 443 | fastdtw | 2016_09_08__11_04_35 | Dynamic time warping (dtw) algorithm with an o(n) time and memory complexity | URL |
| 444 | fastme | 2016_12_22__07_39_46 | A comprehensive, accurate and fast distance-based phylogeny inference program. | URL |
| 445 | fastool | 2016_09_05__13_37_12 | A simple and quick tool to read huge fastq and fasta files (both normal and gzipped) and manipulate them. | URL |
| 446 | fastq-and-furious | 2017_02_09__17_57_38 | None | URL |
| 447 | fastq-multx | 2017_02_03__07_22_37 | Demultiplexes a fastq. capable of auto-determining barcode id's based on a master set fields. keeps multiple reads in-sync during demultiplexing. can verify that the reads are in-sync as well, and fail if they're not. | URL |
| 448 | fastq-screen | 2016_09_04__22_33_16 | Fastq screen allows you to screen a library of sequences in fastq format against a set of sequence databases so you can see if the composition of the library matches with what you expect | URL |
| 449 | fastqc | 2016_11_28__00_19_47 | A quality control tool for high throughput sequence data. | URL |
| 450 | fasttree | 2016_12_31__07_28_18 | Fasttree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences | URL |
| 451 | fastuniq | 2016_11_11__16_25_26 | Fastuniq, a fast de novo duplicates removal tool for paired short reads | URL |
| 452 | fastx_toolkit | 2016_09_06__14_58_12 | None | URL |
| 453 | fermi | 2016_09_05__13_48_55 | A wgs de novo assembler based on the fmd-index for large genomes | URL |
| 454 | fermi2 | 2016_09_05__13_51_31 | Fermi2 focuses on the exploration of fmd-index as a graph. | URL |
| 455 | fftw | 2016_09_06__15_01_03 | The fastest fourier transform in the west. | URL |
| 456 | fgbio | 2017_01_19__10_35_39 | A set of tools for working with genomic and high throughput sequencing data, including umis | URL |
| 457 | ficus | 2017_04_11__17_59_35 | Ficus provides a context manager for matplotlib figures. | URL |
| 458 | fido | 2017_01_13__07_34_09 | A method for protein identification in ms/ms proteomics. think of it like a protein delivery dog. you bring it the scored matches between peptides and spectra, and it fetches a list of proteins ranked by posterior probability by doing clever tricks. | URL |
| 459 | fiji | 2016_10_26__09_50_27 | Fiji is an image processing package—a "batteries-included" distribution of imagej, bundling a lot of plugins which facilitate scientific image analysis. | URL |
| 460 | filechunkio | 2016_09_07__02_00_46 | Filechunkio represents a chunk of an os-level file containing bytes data | URL |
| 461 | find_differential_primers | 2016_12_06__10_07_20 | 'scripts to aid the design of differential primers for diagnostic pcr.' | URL |
| 462 | fisher | 2016_09_07__16_03_12 | Fast fisher's exact test | URL |
| 463 | flaimapper | 2016_11_17__12_14_21 | Flaimapper: detecting small ncrna derived fragments in small rna-seq data | URL |
| 464 | flask-admin | 2016_09_05__14_48_50 | Simple and extensible admin interface framework for flask | URL |
| 465 | flask-basicauth | 2017_04_11__17_59_35 | Http basic access authentication for flask. | URL |
| 466 | flask-bootstrap | 2017_04_11__17_59_35 | An extension that includes bootstrap in your project, without any boilerplate code. | URL |
| 467 | flask-bower | 2016_09_07__05_00_13 | An extension to manage and serve your javascript assets with bower | URL |
| 468 | flask-markdown | 2016_09_07__22_49_50 | Small extension to make using markdown easy | URL |
| 469 | flask-nav | 2016_09_08__03_16_29 | Easily create navigation for flask applications. | URL |
| 470 | flask-potion | 2016_09_07__03_30_25 | Powerful rest api framework for flask and sqlalchemy | URL |
| 471 | flask-script | 2016_09_07__04_06_21 | Scripting support for flask | URL |
| 472 | flask-sqlalchemy | 2016_09_08__07_31_16 | Adds sqlalchemy support to your flask application | URL |
| 473 | flock | 2016_09_05__14_07_38 | None | URL |
| 474 | forked-path | 2016_09_05__02_32_00 | An object oriented file path module | URL |
| 475 | fqtools | 2016_09_05__14_10_01 | An efficient fastq manipulation suite. | URL |
| 476 | fraggenescan | 2017_03_04__08_04_30 | None | URL |
| 477 | freebayes | 2017_02_21__12_49_13 | Bayesian haplotype-based polymorphism discovery and genotyping | URL |
| 478 | fsnviz | 2017_01_24__17_26_32 | Tool for plotting gene fusion events detected by various tools using circos. | URL |
| 479 | ftputil | 2016_09_07__14_45_22 | High-level ftp client library (virtual file system and more) | URL |
| 480 | fuma | 2017_01_23__12_22_18 | Fuma: reporting overlap in rna-seq detected fusion genes | URL |
| 481 | functools32 | 2016_09_07__05_55_46 | Backport of the functools module from python 3.2.3 for use on 2.7 and pypy. | URL |
| 482 | galaxy-lib | 2017_01_24__09_08_37 | Subset of galaxy (http://galaxyproject.org/) core code base designed to be used a library. | URL |
| 483 | galaxy-ops | 2017_02_11__07_51_18 | None | URL |
| 484 | galaxy_sequence_utils | 2017_02_19__16_18_49 | Sequence utilities from the galaxy project | URL |
| 485 | garnet | 2017_03_22__16_07_38 | None | URL |
| 486 | gat | 2017_04_11__17_59_35 | Genomic annotation tool | URL |
| 487 | gatk | 2016_12_14__07_20_31 | The full genome analysis toolkit (gatk) framework, license restricted. | URL |
| 488 | gatk-framework | 2016_09_05__14_22_05 | The core mit-licensed genome analysis toolkit (gatk) framework, free for all uses | URL |
| 489 | gawk | 2016_12_09__20_52_02 | The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. | URL |
| 490 | gb_taxonomy_tools | 2016_09_07__01_02_57 | These are four simple utilities which perform certain manipulations and visualization tasks on genbank taxonomic information. | URL |
| 491 | gclib | 2017_04_06__20_37_14 | None | URL |
| 492 | gdal | 2016_09_06__15_07_37 | Geospatial data abstraction library | URL |
| 493 | gdk-pixbuf | 2017_01_24__11_44_55 | The gdkpixbuf structure — information that describes an image. | URL |
| 494 | gecode | 2017_01_17__14_54_43 | Generic constraint development environment | URL |
| 495 | gemini | 2017_03_20__17_19_50 | A lightweight db framework for disease and population genetics. | URL |
| 496 | genblastg | 2016_09_05__15_07_59 | Genblast is a program suite, consisting of two programs: genblasta and genblastg. genblasta parses local alignments, or high-scoring segment pairs (hsps) produced by local sequence alignment programs such as blast and wu-blast and identify groups of hsps. | URL |
| 497 | geneimpacts | 2017_01_13__19_46_11 | Prioritize effects of variant annotations from vep, snpeff, et al. | URL |
| 498 | genepop | 2016_09_06__15_09_12 | The genepop population genetics package. | URL |
| 499 | genesplicer | 2016_12_08__06_48_25 | Genesplicer : a computational method for splice site prediction | URL |
| 500 | genomedata | 2016_09_08__02_53_15 | Tools for accessing large amounts of genomic data | URL |
| 501 | genometools | 2016_09_07__09_07_28 | Genometools: scripts and classes for working with genomic data. | URL |
| 502 | genomicassertions | 2016_09_07__02_22_10 | A package to test common files in genomics (.vcf.gz, .bam) | URL |
| 503 | genomicconsensus | 2016_11_22__19_26_07 | None | URL |
| 504 | geodl | 2016_08_26__20_25_21 | Dowload fastq files from geo-ncbi with ease | URL |
| 505 | gettext | 2017_04_11__17_59_35 | Gnu gettext | URL |
| 506 | gevent | 2016_09_07__05_32_09 | Coroutine-based network library | URL |
| 507 | gffcompare | 2017_04_07__13_15_51 | None | URL |
| 508 | gffutils | 2016_09_05__15_16_26 | Work with gff and gtf files in a flexible database framework | URL |
| 509 | gfinisher | 2016_11_19__10_52_21 | gfinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of gc skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. | URL |
| 510 | gfold | 2016_09_05__15_19_03 | Find differentially expressed genes from rna-seq data with few replicates using generalized fold changes. | URL |
| 511 | ghmm | 2017_04_09__08_21_00 | None | URL |
| 512 | ghostscript | 2016_09_05__16_26_38 | An interpreter for the postscript language and for pdf. | URL |
| 513 | gimmemotifs | 2017_04_04__09_53_46 | None | URL |
| 514 | git | 2016_07_18__09_44_11 | A distributed version control system | URL |
| 515 | git-lfs | 2016_12_08__16_58_28 | None | URL |
| 516 | glimmer | 2017_03_09__18_38_17 | Glimmer is a system for finding genes in microbial dna | URL |
| 517 | glob2 | 2016_09_08__05_05_21 | Version of the glob module that can capture patterns and supports recursive wildcards | URL |
| 518 | glpk | 2016_09_07__22_36_05 | Gnu linear programming kit | URL |
| 519 | gmap | 2017_02_24__14_00_20 | Genomic mapping and alignment program for mrna and est sequences | URL |
| 520 | gmtk | 2016_09_05__15_39_15 | A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (dgms) and dynamic bayesian networks (dbns) | URL |
| 521 | gnu-wget | 2016_10_26__12_30_50 | Retrieve files using http, https and ftp | URL |
| 522 | gnuplot | 2017_04_11__17_59_35 | Gnuplot, plotting from command line | URL |
| 523 | gnuplot-py | 2016_09_20__13_17_43 | A python interface to the gnuplot plotting program. | URL |
| 524 | go | 2016_03_10__09_11_20 | Go programming language compiler | URL |
| 525 | goatools | 2016_10_16__07_09_28 | Python scripts to find enrichment of go terms | URL |
| 526 | gocr | 2016_09_05__15_45_41 | Gocr is an ocr (optical character recognition) program | URL |
| 527 | goleft | 2017_03_16__10_56_40 | goleft is a collection of bioinformatics tools distributed under mit license in a single static binary | URL |
| 528 | google-api-python-client | 2016_09_08__00_01_24 | None | URL |
| 529 | google-cloud-sdk | 2016_09_05__14_39_49 | command-line interface for google cloud platform products and services | URL |
| 530 | google-sparsehash | 2016_09_06__06_54_29 | Several hash-map implementations. | URL |
| 531 | gprofiler-official | 2017_01_18__08_08_41 | Functional enrichment analysis and more via the g:profiler toolkit | URL |
| 532 | grabix | 2017_01_27__11_54_30 | Grabix leverages the fantastic bgzf library in samtools to provide random access into text files that have been compressed with bgzip. grabix creates it's own index (.gbi) of the bgzipped file. once indexed, one can extract arbitrary lines from the file with the grab command. https://github.com/arq5x/grabix | URL |
| 533 | graftm | 2017_04_08__08_23_57 | None | URL |
| 534 | graph_embed | 2017_04_11__17_59_35 | Compute a 2d embedding of a data matrix given supervised class information. | URL |
| 535 | graphclust-wrappers | 2017_03_24__11_09_26 | The set of individual perl wrappers extracted from graphclust pipeline | URL |
| 536 | graphicsmagick | 2017_01_12__17_03_33 | Graphicsmagick is the swiss army knife of image processing | URL |
| 537 | graphlite | 2016_09_07__06_42_40 | Embedded graph datastore | URL |
| 538 | graphmap | 2017_01_24__11_57_49 | 'a highly sensitive and accurate mapper for long, error-prone reads.' | URL |
| 539 | graphviz | 2017_04_11__17_59_35 | Graph visualization software | URL |
| 540 | grep | 2016_09_05__16_06_10 | Grep searches one or more input files for lines containing a match to a specified pattern | URL |
| 541 | grequests | 2016_09_08__10_56_30 | Requests + gevent | URL |
| 542 | gromacs | 2016_09_05__14_23_37 | Gromacs is a versatile package to perform molecular dynamics. | URL |
| 543 | gseapy | 2016_09_01__13_47_57 | Gene set enrichment analysis in python | URL |
| 544 | gsort | 2016_09_05__16_22_25 | Sort genomic files according to a genomefile | URL |
| 545 | gtf_to_genes | 2017_01_12__07_36_58 | Fast gtf parser | URL |
| 546 | gustaf | 2017_01_28__23_36_36 | Gustaf is a tool primarily designed for multi-split mapping of sequencing reads. | URL |
| 547 | gvcf-regions | 2016_09_05__16_31_24 | Convert a gvcf file in multiple formats into a bed file of callable regions | URL |
| 548 | hap.py | 2017_03_16__10_56_19 | None | URL |
| 549 | hapbin | 2017_04_11__17_59_35 | Hapbin is a collection of tools for efficiently calculating extended haplotype homozygosity (ehh), the integrated haplotype score (ihs) and the cross population extended haplotype homozogysity (xp-ehh) statistic. | URL |
| 550 | hapflk | 2017_03_04__08_07_54 | None | URL |
| 551 | hardklor | 2016_09_28__17_58_22 | analyze mass spectra | URL |
| 552 | hcluster_sg | 2017_03_24__12_40_39 | A tool for hierarchically clustering on a sparse graph | URL |
| 553 | hello | 2016_03_10__21_44_40 | Program providing model for GNU coding standards and practices | URL |
| 554 | hgtools | 2016_09_06__22_40_24 | Classes and setuptools plugin for mercurial and git repositories | URL |
| 555 | hicexplorer | 2017_04_03__10_30_48 | Set of programs to process, analyze and visualize hi-c data | URL |
| 556 | hicup | 2017_01_05__16_56_27 | 'a tool for mapping and performing quality control on hi-c data' | URL |
| 557 | hifive | 2017_02_24__21_12_10 | Python library for normalizing and analyzing hic and 5c data | URL |
| 558 | hisat2 | 2016_09_04__13_34_06 | Graph-based alignment of next generation sequencing reads to a population of genomes | URL |
| 559 | hlama | 2016_11_01__07_15_08 | Simple matching of hts samples based on hla typing | URL |
| 560 | hmmer | 2017_01_26__01_02_11 | Biosequence analysis using profile hidden markov models | URL |
| 561 | homer | 2016_11_01__07_15_48 | Software for motif discovery and next generation sequencing analysis | URL |
| 562 | htsbox | 2016_09_05__17_58_29 | Htsbox is a fork of early htslib. it is a collection of small experimental tools manipulating hts-related files. | URL |
| 563 | htslib | 2017_03_21__10_20_26 | c library for high-throughput sequencing data formats. | URL |
| 564 | httplib2 | 2016_09_06__22_12_25 | A comprehensive http client library. | URL |
| 565 | httpretty | 2016_09_05__23_43_36 | Http client mock for python | URL |
| 566 | hubward | 2016_09_10__03_12_16 | Manage the visualization of large amounts of other people's [often messy] genomics data | URL |
| 567 | hubward-all | 2016_09_08__22_51_37 | Meta-package for hubward including bedtools and ucsc tools | URL |
| 568 | humann2 | 2017_02_08__12_43_57 | Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data | URL |
| 569 | hurry.filesize | 2016_09_05__23_49_19 | A simple python library for human readable file sizes (or anything sized in bytes). | URL |
| 570 | ibdne | 2017_03_16__01_16_15 | None | URL |
| 571 | ibdseq | 2017_03_16__00_34_44 | None | URL |
| 572 | idba | 2016_12_23__07_23_27 | 'idba is a practical iterative de bruijn graph de novo assembler for sequence assembly in bioinformatics.' | URL |
| 573 | idr | 2017_03_22__23_44_40 | The idr (irreproducible discovery rate) framework is a uni?ed approach to measure the reproducibility of ?ndings identi?ed from replicate experiments and provide highly stable thresholds based on reproducibility. | URL |
| 574 | ig-checkfcs | 2017_03_04__10_17_45 | None | URL |
| 575 | ig-flowtools | 2017_03_17__21_33_43 | None | URL |
| 576 | igblast | 2016_09_08__02_49_38 | A tool for analyzing immunoglobulin (ig) and t cell receptor (tr) sequences. | URL |
| 577 | igdiscover | 2016_12_08__15_19_44 | Analyze antibody repertoires and discover new v genes | URL |
| 578 | igvtools | 2016_09_05__11_56_31 | Command line tools for igv | URL |
| 579 | illuminate | 2016_09_08__06_47_45 | Analytics toolkit for illumina sequencer metrics. | URL |
| 580 | impute2 | 2016_05_08__11_30_27 | Genotype imputation and haplotype phasing | URL |
| 581 | infernal | 2017_01_14__13_21_51 | Infernal ("inference of rna alignment") is for searching dna sequence databases for rna structure and sequence similarities. | URL |
| 582 | infinity | 2016_09_06__00_02_36 | All-in-one infinity value for python. can be compared to any object. | URL |
| 583 | inforna | 2016_09_21__18_14_29 | A server for the design of rna sequences that fold into a given pseudo-knot free rna secondary structure. | URL |
| 584 | inheritance | 2016_09_07__20_40_29 | Inheritance models for mendelian diseases | URL |
| 585 | intarna | 2017_03_28__11_20_22 | None | URL |
| 586 | intemap | 2017_02_28__07_31_48 | None | URL |
| 587 | intermine | 2016_09_08__07_54_18 | None | URL |
| 588 | intervalstats | 2017_04_11__17_59_35 | Tool for assessing similarity between sets of intervals | URL |
| 589 | intervaltree | 2016_09_04__07_51_05 | Editable interval tree data structure for python 2 and 3 | URL |
| 590 | intervaltree_bio | 2017_04_02__08_17_32 | None | URL |
| 591 | involucro | 2016_11_13__11_05_51 | Build and deliver software with containers | URL |
| 592 | ipython-cluster-helper | 2017_02_25__11_03_48 | Tool to easily start up an ipython cluster on different schedulers | URL |
| 593 | iqtree | 2017_01_26__07_39_31 | "efficient phylogenomic software by maximum likelihood" | URL |
| 594 | irssi | 2016_03_10__09_11_52 | A modular textUI IRC client with IPv6 support | URL |
| 595 | isodate | 2016_09_06__00_21_07 | An iso 8601 date/time/duration parser and formatter | URL |
| 596 | itk | 2017_03_18__14_41_37 | itk is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. | URL |
| 597 | iva | 2016_12_03__05_30_38 | Iterative virus assembler | URL |
| 598 | jaffa | 2017_03_15__09_27_33 | None | URL |
| 599 | jamm | 2016_09_07__12_16_11 | Jamm is a peak finder for ngs datasets (chip-seq, atac-seq, dnase-seq..etc.) that can integrate replicates and assign peak boundaries accurately. | URL |
| 600 | jannovar-cli | 2017_04_04__14_43_52 | None | URL |
| 601 | java-jdk | 2017_01_12__20_58_07 | The zulu openjdk build. | URL |
| 602 | jbrowse | 2016_11_16__15_55_03 | The jbrowse genome browser | URL |
| 603 | jellyfish | 2016_09_05__12_19_11 | Jellyfish is a tool for fast, memory-efficient counting of k-mers in dna. a k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of dna sequence | URL |
| 604 | jemalloc | 2017_03_20__01_00_42 | None | URL |
| 605 | jmespath | 2016_09_06__22_06_39 | None | URL |
| 606 | jpeg | 2016_11_14__15_13_19 | None | URL |
| 607 | jq | 2016_09_05__12_21_07 | Jq is a lightweight and flexible command-line json processor. | URL |
| 608 | julia | 2017_04_11__17_59_35 | A high-performance dynamic programming language for data science | URL |
| 609 | junit-xml | 2016_11_25__13_08_07 | Creates junit xml test result documents that can be read by tools such as jenkins | URL |
| 610 | kaiju | 2017_02_06__10_25_48 | Fast and sensitive taxonomic classification for metagenomics | URL |
| 611 | kallisto | 2016_12_17__07_19_32 | Quantifying abundances of transcripts from rna-seq data, or more generally of target sequences using high-throughput sequencing reads. | URL |
| 612 | kaptive | 2017_04_07__08_25_43 | None | URL |
| 613 | kat | 2017_03_05__16_34_21 | Kat is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts | URL |
| 614 | keepalive | 2016_09_06__00_32_34 | Urllib keepalive support for python | URL |
| 615 | khmer | 2016_09_06__00_36_08 | Khmer is a library and suite of command line tools for working with dna sequence. it is primarily aimed at short-read sequencing data such as that produced by the illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. | URL |
| 616 | kid | 2016_05_08__11_32_57 | A simple and pythonic xml template language | URL |
| 617 | kiwidist | 2017_01_26__15_25_07 | Combining gene-set analysis with network properties | URL |
| 618 | kmc | 2016_08_26__20_29_58 | K-mer counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. | URL |
| 619 | kmergenie | 2017_03_14__10_02_08 | Kmergenie estimates the best k-mer length for genome de novo assembly | URL |
| 620 | kneaddata | 2016_11_28__07_45_42 | 'kneaddata is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.' | URL |
| 621 | knot | 2016_09_06__16_57_09 | Detection of knots in protein folds. | URL |
| 622 | kobas | 2016_10_28__20_43_24 | None | URL |
| 623 | koeken | 2016_11_28__07_37_22 | 'a linear discriminant analysis (lefse) wrapper.' | URL |
| 624 | kpal | 2016_12_09__07_21_17 | Analysis toolkit and programming library for k-mer profiles | URL |
| 625 | kraken | 2017_04_03__10_37_33 | Kraken is a system for assigning taxonomic labels to short dna sequences, usually obtained through metagenomic studies. | URL |
| 626 | kraken-all | 2016_09_06__15_23_29 | This metapackage installs kraken with optional dependency jellyfish for building kraken databases. | URL |
| 627 | krona | 2017_02_16__03_31_56 | Krona tools is a set of scripts to create krona charts from several bioinformatics tools as well as from text and xml files. | URL |
| 628 | lapack | 2016_09_06__23_28_37 | Linear algebra package | URL |
| 629 | last | 2016_09_05__12_47_36 | Last finds similar regions between sequences, and aligns them. it is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of dna reads). | URL |
| 630 | lastz | 2016_09_14__13_34_24 | Lastz is a program for aligning dna sequences, a pairwise aligne | URL |
| 631 | latentstrainanalysis | 2017_02_09__07_51_43 | None | URL |
| 632 | lefse | 2017_04_07__13_22_16 | "lda effect size (lefse) (segata et. al 2010) is an algorithm for high-dimensional biomarker discovery and explanation that identifies genomic features (genes, pathways, or taxa) characterizing the differences between two or more biological conditions." | URL |
| 633 | lemon | 2017_02_21__10_59_55 | None | URL |
| 634 | lftp | 2016_07_18__20_45_46 | LFTP is sophisticated ftp/http client | URL |
| 635 | libdb | 2016_09_08__08_14_43 | The berkeley db embedded database system. | URL |
| 636 | libgd | 2016_11_15__08_50_45 | None | URL |
| 637 | libgtextutils | 2016_09_06__15_31_54 | None | URL |
| 638 | libidn | 2017_03_11__08_03_16 | None | URL |
| 639 | libsbml | 2017_04_11__17_59_35 | Libsbml python api. libsbml is a library for reading, writing and manipulating the systems biology markup language (sbml). | URL |
| 640 | libxml2 | 2017_04_11__17_59_35 | Libxml2 is the xml c parser and toolkit developed for the gnome project (but usable outside of the gnomeplatform), it is free software available under the mit license. xml itself is a metalanguage to design markuplanguages, i.e. text language where semantic and structure are added to the content using extra "markup"information enclosed between angle brackets. html is the most well-known markup language. though the libraryis written in c a variety of language bindings make it available in other environments. | URL |
| 641 | lighter | 2016_06_04__17_00_09 | Ighter is a kmer-based error correction method for whole genome sequencing data | URL |
| 642 | links | 2016_09_05__12_49_59 | long interval nucleotide k-mer scaffolder | URL |
| 643 | locarna | 2017_03_05__13_59_43 | Multiple alignment of rnas | URL |
| 644 | lofreq | 2016_09_05__12_52_53 | A fast and sensitive variant-caller for inferring snvs and indels from next-generation sequencing data | URL |
| 645 | log4cpp | 2017_01_05__07_42_44 | "log4cpp is library of c++ classes for flexible logging to files, syslog, idsa and other destinations" | URL |
| 646 | logbook | 2016_09_06__00_57_37 | A logging replacement for python | URL |
| 647 | lsd | 2016_11_23__07_07_35 | None | URL |
| 648 | lumpy-sv | 2016_09_14__07_20_34 | A general probabilistic framework for structural variant discovery | URL |
| 649 | lz4-bin | 2016_09_09__06_34_48 | Extremely fast compression application | URL |
| 650 | m4 | 2016_03_10__09_12_43 | None | URL |
| 651 | maaslin | 2016_11_16__01_13_14 | Maaslin is a multivariate statistical framework that finds associations between clinical metadata and microbial community abundance or function. | URL |
| 652 | macs2 | 2016_09_07__00_43_43 | Macs -- model-based analysis of chip-seq | URL |
| 653 | mafft | 2016_12_25__07_35_23 | Multiple alignment program for amino acid or nucleotide sequences based on fast fourier transform | URL |
| 654 | mageck | 2017_02_17__12_28_16 | Model-based analysis of genome-wide crispr-cas9 knockout. | URL |
| 655 | mageck-vispr | 2016_09_20__13_47_36 | mageck-vispr is a comprehensive quality control, analysis and visualization workflow for crispr/cas9 screens based on mageck, vispr, snakemake, fastqc and cutadapt. | URL |
| 656 | manormfast | 2017_01_27__07_48_40 | Fast, memory-intensive version of manorm | URL |
| 657 | manta | 2016_12_07__12_42_56 | structural variant and indel caller for mapped sequencing data | URL |
| 658 | mapdamage2 | 2016_10_07__13_01_39 | Mapdamage: tracking and quantifying damage patterns in ancient dna sequences http://geogenetics.ku.dk/all_literature/mapdamage/ | URL |
| 659 | mapsplice | 2016_09_05__14_09_46 | Mapsplice is a software for mapping rna-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations. | URL |
| 660 | mash | 2016_05_03__22_06_40 | Fast sequence distance estimator that uses minhash | URL |
| 661 | mashmap | 2017_02_03__11_52_10 | 'a fast and approximate long read mapper' | URL |
| 662 | mason | 2017_01_28__16_06_17 | Mason is a collection of tools for the simulation of biological sequences. | URL |
| 663 | mathstats | 2016_09_07__18_36_20 | Statistical functions, goodness-of-fit tests and special and special distributions not implemented in scipy/numpy . | URL |
| 664 | matplotlib | 2016_09_26__23_13_07 | None | URL |
| 665 | mawk | 2016_09_05__14_11_19 | Mawk is an interpreter for the awk programming language. | URL |
| 666 | maxbin2 | 2017_03_02__03_16_54 | "maxbin is software for binning assembled metagenomic sequences based on an expectation-maximization algorithm." | URL |
| 667 | maxentscan | 2016_12_08__07_13_26 | Maxentscan is based on the approach for modeling the sequences of short sequence motifs such as those involved in rna splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions. this method is based on the 'maximum entropy principle' and generalizes most previous probabilistic models of sequence motifs such as weight matrix models and inhomogeneous markov models. | URL |
| 668 | mbuffer | 2016_09_05__14_13_40 | Mbuffer is a tool for buffering data streams with a large set of unique features | URL |
| 669 | mc | 2016_07_18__20_46_14 | A filemanager/shell that emulates Norton Commander | URL |
| 670 | mcl | 2016_10_29__07_25_22 | Mcl - a cluster algorithm for graphs | URL |
| 671 | medusa | 2017_04_11__17_59_35 | Medusa is an approach to detect size-k modules of objects that, taken together, appear most significant to another set of objects. it builds on collective matrix factorization to derive different semantics, and it formulates the growing of the modules as a submodular optimization program. | URL |
| 672 | megagta | 2016_11_02__21_36_06 | Hmm-guided metagenomic gene-targeted assembler using iterative de bruijn graphs | URL |
| 673 | megahit | 2017_01_04__07_30_35 | Megahit: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph | URL |
| 674 | melt | 2016_09_06__08_17_43 | A nucleotide melt temp calculator | URL |
| 675 | meme | 2017_01_12__06_24_00 | Motif based sequence analysis tools | URL |
| 676 | mendelscan | 2016_09_05__14_37_37 | Analyze exome data for mendelian disorders. | URL |
| 677 | mercat | 2017_02_24__00_40_51 | None | URL |
| 678 | merfishtools | 2017_01_28__23_41_45 | "merfishtools implement a bayesian framework for accurately predicting | URL |
| 679 | mergevcf | 2017_04_03__08_22_15 | None | URL |
| 680 | metacluster | 2016_12_06__08_38_58 | metacluster5.1 is a new software for binning short pair-end reads | URL |
| 681 | metametamerge | 2016_12_16__07_24_14 | Merging module of the metameta pipeline | URL |
| 682 | metaphlan2 | 2017_02_19__18_09_35 | Metaphlan is a computational tool for profiling the composition of microbial communities (bacteria, archaea, eukaryotes and viruses) from metagenomic shotgun sequencing data with species level resolution. from version 2.0 metaphlan is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. | URL |
| 683 | metaprob | 2017_02_27__19_34_55 | None | URL |
| 684 | metaseq-all | 2017_04_11__17_59_35 | Meta-package for metaseq including bedtools and ucsc tools | URL |
| 685 | metasv | 2016_09_06__23_52_36 | An accurate and integrative structural-variant caller for next generation sequencing | URL |
| 686 | metavelvet | 2016_09_05__15_05_30 | Metavelvet : an extension of velvet assembler to de novo metagenome assembly from short sequence reads | URL |
| 687 | metavelvet-sl | 2017_03_16__00_18_24 | Metavelvet-sl : an extension of velvet assembler to de novo metagenomic assembler utilizing supervised learning | URL |
| 688 | metavelvet-sl-feature-extraction | 2017_03_16__09_57_07 | Perl libraries that do feature extraction for metavelvet-sl | URL |
| 689 | metavelvet-sl-pipeline | 2017_03_15__21_51_35 | None | URL |
| 690 | metawatt | 2017_03_03__08_31_04 | None | URL |
| 691 | methyldackel | 2017_01_27__14_04_44 | A (mostly) universal methylation extractor for bs-seq experiments. formerly named pileometh. | URL |
| 692 | metilene | 2016_05_17__18_22_20 | Fast and sensitive detection of differential dna methylation | URL |
| 693 | mgkit | 2017_04_11__17_59_35 | 'metagenomics framework' | URL |
| 694 | mgltools | 2016_09_05__22_34_58 | Mgltools is an program for visualization and analisys of molecular structures. | URL |
| 695 | mhap | 2016_09_05__15_09_56 | Mhap: minhash alignment protocol. a tool for finding overlaps of long-read sequences (such as pacbio or nanopore) in bioinformatics. | URL |
| 696 | migmap | 2016_09_06__15_55_54 | A wrapper for igblast v-(d)-j mapping tool designed to facilitate analysis immune receptor libraries profiled using high-throughput sequencing. | URL |
| 697 | mimodd | 2016_10_25__07_10_54 | tools for mutation identification in model organism genomes | URL |
| 698 | minced | 2016_09_05__15_14_50 | Minced - mining crisprs in environmental datasets | URL |
| 699 | minepy | 2017_04_02__08_20_49 | None | URL |
| 700 | minialign | 2017_03_11__10_02_52 | "fast and accurate alignment tool for pacbio and nanopore long reads." | URL |
| 701 | miniasm | 2017_03_28__15_13_05 | Ultrafast de novo assembly for long noisy reads (though having no consensus step) | URL |
| 702 | mir-prefer | 2017_02_03__04_08_41 | None | URL |
| 703 | mira | 2016_09_05__15_18_34 | Mira is a whole genome shotgun and est sequence assembler for sanger, 454, solexa (illumina), iontorrent data and pacbio (the later at the moment only ccs and error-corrected clr reads) | URL |
| 704 | miranda | 2016_09_05__15_25_16 | An algorithm for finding genomic targets for micrornas | URL |
| 705 | mirdeep2 | 2017_03_17__17_06_13 | A completely overhauled tool which discovers microrna genes by analyzing sequenced rnas | URL |
| 706 | mksh | 2016_03_10__09_13_01 | MirBSD KSH Shell | URL |
| 707 | mlst | 2016_09_07__06_33_51 | Scan contig files against pubmlst typing schemes | URL |
| 708 | mmtf-python | 2016_12_08__08_39_56 | A decoding libary for the pdb mmtf format | URL |
| 709 | mobster | 2017_03_31__08_19_56 | None | URL |
| 710 | moca | 2017_02_04__20_25_43 | Tool for motif conservation analysis | URL |
| 711 | mono | 2016_11_12__16_05_35 | None | URL |
| 712 | moreutils | 2016_09_06__06_58_20 | A growing collection of the unix tools that nobody thought to write long ago when unix was young | URL |
| 713 | mosaik | 2016_09_05__15_54_42 | Mosaik is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. | URL |
| 714 | mothur | 2017_02_28__09_29_54 | None | URL |
| 715 | moto | 2016_09_05__16_02_19 | A library that allows your python tests to easily mock out the boto library | URL |
| 716 | motus | 2016_12_08__12_38_20 | 'motus metagenomic species profiling using universal phylogenetic marker genes' | URL |
| 717 | mpa-portable | 2017_03_04__08_10_52 | None | URL |
| 718 | mreps | 2017_04_11__17_59_35 | Mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in dna sequences. | URL |
| 719 | ms | 2016_09_05__16_05_40 | Generates random independent samples according to a simple wright-fisher neutral model. | URL |
| 720 | msgf_plus | 2017_01_12__06_44_18 | Ms-gf+ is a new ms/ms database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of ms instruments and different experimental protocols). | URL |
| 721 | msms | 2016_09_05__04_48_26 | Msms is a program written in the c programming language to compute molecular surfaces. | URL |
| 722 | msprime | 2017_03_09__11_49_12 | A fast and accurate coalescent simulator. | URL |
| 723 | msstitch | 2017_02_10__20_22_01 | Ms proteomics post processing utilities | URL |
| 724 | mtr | 2016_03_10__09_13_22 | Full screen ncurses traceroute tool | URL |
| 725 | mugsy | 2016_09_06__16_03_34 | Mugsy is a multiple whole genome aligner. | URL |
| 726 | multigps | 2017_04_04__05_45_29 | None | URL |
| 727 | multiprocess | 2016_09_07__12_51_17 | Package for using processes which mimics the threading module | URL |
| 728 | multiqc | 2017_03_07__11_16_48 | Create aggregate bioinformatics analysis reports across many samples and tools | URL |
| 729 | multiqc-bcbio | 2017_02_09__12_28_20 | Multiqc plugin for bcbio report visualization. | URL |
| 730 | munkres | 2017_03_18__11_16_42 | None | URL |
| 731 | muscle | 2016_11_02__20_35_48 | "muscle: multiple sequence alignment with high accuracy and high throughput" | URL |
| 732 | music | 2017_03_27__08_11_45 | None | URL |
| 733 | musicc | 2016_10_30__11_34_52 | Musicc: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. | URL |
| 734 | mvicuna | 2016_09_05__16_21_49 | M-vicuna is a modularized version of vicuna, a de novo assembly program targeting populations with high mutation rates | URL |
| 735 | mygene | 2017_03_02__18_24_11 | Python client for mygene.info services. | URL |
| 736 | myriad | 2016_09_28__17_57_58 | Simple distributed computing. | URL |
| 737 | mysql-connector-c | 2016_11_15__14_33_01 | Mysql connector/c, the c interface for communicating with mysql servers. | URL |
| 738 | mysqlclient | 2016_11_15__16_54_45 | Python interface to mysql | URL |
| 739 | mzml2isa | 2016_09_05__16_27_48 | Mzml2isa - mzml to isa-tab parsing tool | URL |
| 740 | mztosqlite | 2016_12_24__07_31_06 | None | URL |
| 741 | nanoblaster | 2016_09_05__16_30_08 | Basic local alignment and search tool for oxford nanopore long sequences | URL |
| 742 | nanocall | 2016_10_08__12_32_53 | An oxford nanopore basecaller | URL |
| 743 | nanonet | 2017_02_25__19_36_23 | nanonet provides recurrent neural network basecalling for oxford nanopore minion data. | URL |
| 744 | nanopolish | 2017_04_01__21_16_27 | Signal-level algorithms for minion data | URL |
| 745 | nanoraw | 2017_01_19__13_25_04 | Analysis of nanopore sequencing data. | URL |
| 746 | nanosim | 2017_02_15__23_18_12 | None | URL |
| 747 | nanosimh | 2017_03_02__16_01_24 | None | URL |
| 748 | nasm | 2016_09_05__14_54_09 | Nasm, the netwide assembler. | URL |
| 749 | nasp | 2016_09_06__07_58_04 | the northern arizona snp pipeline (nasp) | URL |
| 750 | ncbi-genome-download | 2016_12_07__18_42_12 | 'download genome files from the ncbi ftp server.' | URL |
| 751 | netcdf-fortran | 2017_01_18__08_09_25 | Unidata netcdf fortran library | URL |
| 752 | netifaces | 2016_09_08__01_20_45 | None | URL |
| 753 | networkxgmml | 2016_09_06__16_08_35 | Xgmml parser for networkx | URL |
| 754 | newt | 2016_09_06__21_18_27 | None | URL |
| 755 | nextflow | 2017_04_07__12_49_58 | A dsl for data-driven computational pipelines http://nextflow.io | URL |
| 756 | nextgenmap | 2017_01_16__07_36_03 | nextgenmap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. | URL |
| 757 | nglview | 2017_03_19__22_06_06 | an ipython widget to interactively view molecular structures and trajectories. utilizes the embeddable ngl viewer for rendering. | URL |
| 758 | ngmlr | 2017_03_30__09_45_47 | ngmlr is a long-read mapper desigend to align pacbilo or oxford nanopore to a reference genome optimized for structural variation detection | URL |
| 759 | ngs-disambiguate | 2016_11_21__11_02_39 | Disambiguation algorithm for reads aligned to human and mouse genomes using tophat or bwa mem | URL |
| 760 | ngseqbasic | 2017_03_02__09_59_28 | None | URL |
| 761 | ngsutils | 2017_04_03__08_24_03 | None | URL |
| 762 | nmrglue | 2017_02_08__07_54_57 | None | URL |
| 763 | nmrml2isa | 2016_09_05__03_09_02 | Nmrml2isa - nmrml to isa-tab parsing tool | URL |
| 764 | nmrpro | 2017_02_09__07_55_38 | None | URL |
| 765 | nonpareil | 2016_09_28__15_08_32 | Estimate average coverage and create nonpareil curves for metagenomic datasets. | URL |
| 766 | nose-capturestderr | 2016_09_06__02_29_20 | Nose plugin for capturing stderr. | URL |
| 767 | novoalign | 2017_02_28__07_08_06 | Powerful tool designed for mapping of short reads onto a reference genome from illumina, ion torrent, and 454 ngs platforms | URL |
| 768 | npyscreen | 2017_02_12__07_54_57 | None | URL |
| 769 | nspdk | 2016_12_08__07_13_54 | Neighborhood subgraph pairwise distance kernel (nspdk). | URL |
| 770 | ntcard | 2017_02_04__11_31_13 | None | URL |
| 771 | nucleoatac | 2017_01_19__07_46_13 | 'python package for calling nucleosomes using atac-seq data. also includes general scripts for working with paired-end atac-seq data (or potentially other paired-end data).' | URL |
| 772 | nudup | 2017_02_25__10_50_58 | None | URL |
| 773 | oauth2client | 2016_09_07__05_01_04 | Client library for oauth 2.0 | URL |
| 774 | obitools | 2017_03_22__08_11_14 | None | URL |
| 775 | ococo | 2016_08_30__15_16_46 | Ococo, the first online consensus caller. | URL |
| 776 | ocrad | 2016_09_08__06_58_55 | Ocrad is an optical character recognition program. | URL |
| 777 | ogdf | 2017_02_25__10_37_17 | None | URL |
| 778 | oligotyping | 2016_10_07__16_06_44 | The oligotyping and minimum entropy decomposition (med) pipeline for the analysis of marker gene amplicons | URL |
| 779 | onto2nx | 2017_03_11__08_04_45 | None | URL |
| 780 | openbabel | 2016_11_05__17_01_32 | A chemical toolbox designed to speak the many languages of chemical data | URL |
| 781 | openmg | 2016_05_19__09_15_55 | Exhaustive generation of chemical structures | URL |
| 782 | openms | 2017_01_23__22_37_52 | openms is an open-source software c++ library for lc-ms data management and analyses | URL |
| 783 | openpyxl | 2016_09_06__03_06_48 | A python library to read/write excel 2007 xlsx/xlsm files | URL |
| 784 | openslide | 2017_02_12__07_56_27 | None | URL |
| 785 | opsin | 2016_05_09__06_48_48 | Opsin is a java(1.6+) library for iupac name-to-structure conversion offering high recall and precision on organic chemical nomenclature. | URL |
| 786 | optbuild | 2016_09_06__03_13_00 | Build command lines for external programs | URL |
| 787 | optitype | 2017_03_17__08_12_42 | Precision hla typing from next-generation sequencing data | URL |
| 788 | optplus | 2016_09_06__03_16_26 | Additional options for optparse | URL |
| 789 | orthofinder | 2017_02_15__12_45_19 | Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy! | URL |
| 790 | pacbio_falcon | 2017_01_16__07_37_38 | "a set of tools for fast aligning long reads for consensus and assembly" | URL |
| 791 | paladin | 2017_02_27__12_49_42 | None | URL |
| 792 | paml | 2017_01_26__13_15_37 | A package of programs for phylogenetic analyses of dna or protein sequences using maximum likelihood. | URL |
| 793 | pancake | 2016_11_21__11_26_28 | A data structure for pangenomes -- identification of singletons and core regions dependent on pairwise sequence similarities | URL |
| 794 | pandaseq | 2017_03_09__08_04_13 | None | URL |
| 795 | pandoc | 2016_10_08__21_02_18 | Pandoc a universal document converter | URL |
| 796 | pantools | 2016_11_05__07_07_24 | pantools is a disk-based java application for computational pan-genomics | URL |
| 797 | parafly | 2016_09_08__01_58_03 | Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. success/failure is captured, and failed commands are retained and reported. | URL |
| 798 | parallel | 2017_01_27__22_27_29 | Gnu parallel is a shell tool for executing jobs in parallel using one or more computers. | URL |
| 799 | paralyzer | 2016_12_03__07_20_23 | We developed the paralyzer algorithm to generate a high resolution map of interaction sites between rna-binding proteins and their targets. the algorithm utilizes the deep sequencing reads generated by par-clip (photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation) protocol.the use of photoactivatable nucleotides in the par-clip protocol results in more efficient crosslinking between the rna-binding protein and its target relative to other clip methods; in addition a nucleotide substitution occurs at the site of crosslinking, providing for single-nucleotide resolution binding information. paralyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of protein-rna interaction sites. | URL |
| 800 | paraview | 2017_01_10__17_21_38 | paraview is an open-source, multi-platform data analysis and visualization application based on visualization toolkit (vtk). | URL |
| 801 | pash | 2017_01_27__07_50_12 | A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel dna sequencing | URL |
| 802 | pasta | 2017_01_10__17_30_28 | An implementation of the pasta (practical alignment using sate and transitivity) algorithm | URL |
| 803 | pathoscope | 2016_12_16__07_25_58 | Species identification and strain attribution with unassembled sequencing data | URL |
| 804 | pathtools | 2016_09_06__03_21_19 | File system general utilities | URL |
| 805 | pbbam | 2017_02_25__15_37_53 | pacbio bam c++ library, with swig bindings | URL |
| 806 | pbcommand | 2016_11_18__07_09_29 | 'library and tools for interfacing to pacbio pbsmrtpipe workflow engine.' | URL |
| 807 | pbcore | 2016_11_18__07_13_35 | 'a python library for reading and writing pacbio data files' | URL |
| 808 | pbdagcon | 2017_02_25__18_38_51 | None | URL |
| 809 | pbgzip | 2016_09_06__16_11_55 | Parallel block gzip | URL |
| 810 | pbh5tools | 2016_11_18__20_44_24 | 'a swiss-army knife for interrogating pacbio® hdf5 files (cmp.h5, bas.h5).' | URL |
| 811 | pdfkit | 2016_09_06__03_27_33 | Wkhtmltopdf python wrapper to convert html to pdf using the webkit rendering engine and qt | URL |
| 812 | peakranger | 2017_02_19__12_20_54 | Peakranger is a multi-purporse software suite for analyzing next-generation sequencing (ngs) data. | URL |
| 813 | peakzilla | 2016_09_08__03_59_15 | Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor chip-seq and chip-exo experiments at hight accuracy and resolution. | URL |
| 814 | ped_parser | 2016_09_06__03_34_58 | A ped file parser. | URL |
| 815 | peewee | 2016_09_06__04_08_44 | A little orm | URL |
| 816 | pepnovo | 2016_09_29__22_05_55 | Pepnovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data | URL |
| 817 | pepr | 2017_03_08__12_44_00 | Peak-calling and prioritization pipeline for replicated chip-seq data | URL |
| 818 | peptide-shaker | 2017_03_22__22_41_49 | | | URL |
| 819 | percolator | 2017_03_09__08_04_58 | None | URL |
| 820 | perl | 2016_09_05__21_12_09 | Perl Language | URL |
| 821 | perl-aceperl | 2016_09_07__12_06_57 | Object-oriented access to acedb databases | URL |
| 822 | perl-algorithm-dependency | 2016_11_07__23_17_02 | Base class for implementing various dependency trees | URL |
| 823 | perl-algorithm-diff | 2016_09_07__23_18_15 | Compute `intelligent' differences between two files / lists but use the old (<=0.59) interface. | URL |
| 824 | perl-algorithm-munkres | 2016_09_08__06_58_17 | Munkres.pm | URL |
| 825 | perl-aliased | 2017_03_03__08_17_40 | None | URL |
| 826 | perl-apache-test | 2016_11_09__06_48_27 | Special tests sequence failure finder | URL |
| 827 | perl-app-cpanminus | 2017_01_27__22_27_10 | Get, unpack, build and install modules from cpan | URL |
| 828 | perl-appconfig | 2017_04_11__17_59_35 | Appconfig is a bundle of perl5 modules for reading configuration files and parsing command line arguments. | URL |
| 829 | perl-archive-tar | 2017_02_24__10_40_07 | Manipulates tar archives | URL |
| 830 | perl-archive-zip | 2017_03_06__11_47_54 | Provide an interface to zip archive files | URL |
| 831 | perl-array-compare | 2016_09_08__10_09_38 | Perl extension for comparing arrays. | URL |
| 832 | perl-array-utils | 2016_10_30__11_35_53 | Small utils for array manipulation | URL |
| 833 | perl-attribute-handlers | 2017_02_24__10_30_13 | None | URL |
| 834 | perl-authen-sasl-saslprep | 2016_09_07__01_31_59 | A stringprep profile for user names and passwords (rfc 4013) | URL |
| 835 | perl-autoloader | 2017_03_06__11_46_51 | None | URL |
| 836 | perl-b | 2017_02_24__10_41_22 | None | URL |
| 837 | perl-b-hooks-endofscope | 2017_03_04__08_11_28 | None | URL |
| 838 | perl-base | 2017_02_24__10_26_08 | None | URL |
| 839 | perl-bio-asn1-entrezgene | 2016_09_05__17_53_42 | Regular expression-based perl parser for ncbi entrez gene | URL |
| 840 | perl-bio-db-hts | 2016_09_30__19_49_06 | Read files using htslib including bam/cram, tabix and bcf database files | URL |
| 841 | perl-bio-db-sam | 2017_04_11__17_59_35 | Read sam/bam database files | URL |
| 842 | perl-bio-featureio | 2016_09_07__23_36_22 | Modules for reading, writing, and manipulating sequence features | URL |
| 843 | perl-bio-phylo | 2017_04_11__17_59_35 | An object-oriented perl toolkit for analyzing and manipulating phyloinformatic data. | URL |
| 844 | perl-bio-samtools | 2016_09_05__18_01_25 | Read sam/bam files | URL |
| 845 | perl-bioperl | 2016_09_07__13_02_46 | Bioinformatics toolkit | URL |
| 846 | perl-bioperl-core | 2016_11_11__15_43_39 | "core" packages for the bioperl toolkit; you really should install perl-bioperl. | URL |
| 847 | perl-bioperl-run | 2016_09_08__07_26_09 | Bioperl-run - wrapper toolkit | URL |
| 848 | perl-biox-workflow | 2016_09_05__18_20_53 | Template away your bioinformatics workflows. | URL |
| 849 | perl-biox-workflow-plugin-filedetails | 2016_09_05__00_54_30 | Get metadata for files in directories processed by biox::workflow | URL |
| 850 | perl-biox-workflow-plugin-fileexists | 2016_09_05__18_17_11 | A plugin to biox::workflow | URL |
| 851 | perl-bit-vector | 2016_09_05__18_23_11 | Efficient bit vector, set of integers and "big int" math library | URL |
| 852 | perl-blib | 2017_02_24__10_24_32 | None | URL |
| 853 | perl-bloom-faster | 2016_09_07__00_10_41 | Perl extension for the c library libbloom. | URL |
| 854 | perl-border-style | 2017_01_05__07_50_48 | Border style structure | URL |
| 855 | perl-btlib | 2016_11_02__21_36_42 | Binary search tree library | URL |
| 856 | perl-canary-stability | 2016_09_05__18_25_24 | Canary to check perl compatibility for schmorp's modules | URL |
| 857 | perl-capture-tiny | 2016_09_07__11_27_25 | Capture stdout and stderr from perl, xs or external programs | URL |
| 858 | perl-cgi | 2016_09_05__18_27_20 | A generic file fetching mechanism | URL |
| 859 | perl-class-accessor | 2016_11_09__08_36_01 | Automated accessor generation | URL |
| 860 | perl-class-data-inheritable | 2016_09_05__17_44_27 | Inheritable, overridable class data | URL |
| 861 | perl-class-inspector | 2016_09_05__18_29_05 | Get information about a class and its structure | URL |
| 862 | perl-class-load | 2017_01_19__10_37_00 | A working (require "class::name") and more | URL |
| 863 | perl-class-load-xs | 2017_01_19__10_37_19 | Xs implementation of parts of class::load | URL |
| 864 | perl-class-method-modifiers | 2016_09_05__18_31_07 | Provides moose-like method modifiers | URL |
| 865 | perl-class-std | 2016_09_05__18_35_17 | Support for creating standard "inside-out" classes | URL |
| 866 | perl-class-std-fast | 2016_09_08__10_30_52 | Faster but less secure than class::std | URL |
| 867 | perl-clone | 2016_09_05__18_37_32 | Recursively copy perl datatypes | URL |
| 868 | perl-clone-pp | 2017_01_05__07_51_34 | Recursively copy perl datatypes | URL |
| 869 | perl-color-theme | 2017_01_05__07_52_26 | Color theme structure | URL |
| 870 | perl-common-sense | 2016_09_05__18_39_33 | Sane defaults for perl programs | URL |
| 871 | perl-compress-raw-bzip2 | 2016_11_09__08_36_38 | Low-level interface to bzip2 compression library | URL |
| 872 | perl-compress-raw-zlib | 2016_09_07__14_44_04 | Low-level interface to zlib compression library | URL |
| 873 | perl-config-any | 2016_08_31__13_07_18 | Load configuration from different file formats, transparently | URL |
| 874 | perl-config-autoconf | 2016_09_07__20_22_05 | A module to implement some of autoconf macros in pure perl. | URL |
| 875 | perl-config-simple | 2017_02_08__09_55_35 | None | URL |
| 876 | perl-config-tiny | 2016_11_07__23_17_46 | Read/write .ini style files with as little code as possible | URL |
| 877 | perl-convert-binary-c | 2016_09_05__18_41_43 | Binary data conversion using c types | URL |
| 878 | perl-convert-binhex | 2016_09_05__18_44_13 | Extract data from macintosh binhex files | URL |
| 879 | perl-cpan-meta | 2016_09_08__08_10_58 | The distribution metadata for a cpan dist | URL |
| 880 | perl-cpan-meta-check | 2016_09_05__18_47_05 | Verify requirements in a cpan::meta object | URL |
| 881 | perl-cpan-meta-validator | 2017_02_23__09_04_26 | None | URL |
| 882 | perl-cpan-shell | 2017_02_24__10_37_19 | None | URL |
| 883 | perl-crypt-openssl-random | 2017_03_03__08_02_46 | None | URL |
| 884 | perl-crypt-openssl-rsa | 2017_03_03__08_03_29 | None | URL |
| 885 | perl-crypt-rc4 | 2016_09_05__18_49_18 | Perl implementation of the rc4 encryption algorithm | URL |
| 886 | perl-data-optlist | 2016_11_09__08_37_32 | Parse and validate simple name/value option pairs | URL |
| 887 | perl-data-utilities | 2017_03_05__08_32_26 | None | URL |
| 888 | perl-data-uuid | 2016_09_05__18_55_40 | Globally/universally unique identifiers (guids/uuids) | URL |
| 889 | perl-data-walk | 2017_03_05__08_32_46 | None | URL |
| 890 | perl-date-format | 2017_02_24__10_31_47 | None | URL |
| 891 | perl-date-manip | 2016_12_20__07_24_45 | Date manipulation routines | URL |
| 892 | perl-datetime | 2017_03_08__08_07_36 | None | URL |
| 893 | perl-datetime-format-strptime | 2017_03_15__08_08_19 | None | URL |
| 894 | perl-datetime-locale | 2017_03_08__08_08_33 | None | URL |
| 895 | perl-datetime-timezone | 2017_03_08__08_09_28 | None | URL |
| 896 | perl-db-file | 2016_09_05__19_03_57 | Perl5 access to berkeley db version 1.x. | URL |
| 897 | perl-dbd-pg | 2016_11_08__13_14_33 | Postgresql database driver for the dbi module | URL |
| 898 | perl-dbd-sqlite | 2016_09_05__19_00_18 | Self contained rdbms in a dbi driver | URL |
| 899 | perl-dbi | 2016_11_07__22_56_41 | Database independent interface for perl | URL |
| 900 | perl-dbm-deep | 2016_11_08__07_12_33 | A pure perl multi-level hash/array dbm that supports transactions | URL |
| 901 | perl-devel-checkbin | 2016_11_09__08_38_07 | Check that a command is available | URL |
| 902 | perl-devel-globaldestruction | 2016_09_05__19_05_55 | Provides function returning the equivalent of ${^global_phase} eq 'destruct' for older perls. | URL |
| 903 | perl-devel-stacktrace | 2016_09_05__19_07_58 | An object representing a stack trace | URL |
| 904 | perl-digest-hmac | 2017_01_30__12_45_32 | Keyed-hashing for message authentication | URL |
| 905 | perl-digest-md5 | 2017_02_24__10_32_36 | 'perl interface to the md-5 algorithm' | URL |
| 906 | perl-digest-perl-md5 | 2016_09_05__19_12_03 | Perl implementation of rivest's md5 algorithm | URL |
| 907 | perl-digest-sha | 2017_02_24__10_25_45 | None | URL |
| 908 | perl-dist-checkconflicts | 2016_09_05__19_14_06 | Declare version conflicts for your dist | URL |
| 909 | perl-dynaloader | 2017_02_23__09_04_48 | None | URL |
| 910 | perl-email-date-format | 2016_09_05__19_15_58 | Produce rfc 2822 date strings | URL |
| 911 | perl-encode-locale | 2017_01_30__12_46_09 | Determine the locale encoding | URL |
| 912 | perl-error | 2016_09_05__19_19_41 | Error/exception handling in an oo-ish way | URL |
| 913 | perl-eval-closure | 2017_03_04__16_53_21 | None | URL |
| 914 | perl-excel-writer-xlsx | 2016_09_05__14_18_42 | Create a new file in the excel 2007+ xlsx format. | URL |
| 915 | perl-exception-class | 2016_09_05__14_21_31 | A module that allows you to declare real exception classes in perl | URL |
| 916 | perl-exporter-tidy | 2016_09_07__13_36_06 | Another way of exporting symbols | URL |
| 917 | perl-exporter-tiny | 2016_09_05__14_23_32 | Exporter with the features of sub::exporter but only core dependencies | URL |
| 918 | perl-extutils-config | 2016_09_05__14_26_17 | A wrapper for perl's configuration | URL |
| 919 | perl-extutils-helpers | 2016_09_05__14_29_34 | Various portability utilities for module builders | URL |
| 920 | perl-extutils-installpaths | 2016_09_08__01_13_40 | Build.pl install path logic made easy | URL |
| 921 | perl-extutils-makemaker | 2017_03_06__11_44_21 | Create a module makefile | URL |
| 922 | perl-extutils-manifest | 2017_02_24__10_35_26 | Utilities to write and check a manifest file | URL |
| 923 | perl-file-chdir | 2016_11_09__06_51_29 | A more sensible way to change directories | URL |
| 924 | perl-file-compare | 2017_02_23__09_02_44 | None | URL |
| 925 | perl-file-details | 2016_11_09__08_38_39 | File details in an object, stat, hash, etc.. | URL |
| 926 | perl-file-fetch | 2016_09_05__14_32_06 | A generic file fetching mechanism | URL |
| 927 | perl-file-find | 2017_02_24__10_37_44 | None | URL |
| 928 | perl-file-find-rule | 2017_03_30__08_31_31 | Alternative interface to file::find | URL |
| 929 | perl-file-grep | 2016_10_30__11_36_32 | Find matches to a pattern in a series of files and related functions | URL |
| 930 | perl-file-homedir | 2016_11_09__08_39_22 | Find your home and other directories on any platform | URL |
| 931 | perl-file-listing | 2016_09_08__09_47_10 | Parse directory listing | URL |
| 932 | perl-file-path | 2017_03_06__11_47_13 | Create or remove directory trees | URL |
| 933 | perl-file-sharedir | 2016_09_05__14_39_34 | Locate per-dist and per-module shared files | URL |
| 934 | perl-file-sharedir-install | 2016_09_05__14_36_35 | Install shared files | URL |
| 935 | perl-file-slurp | 2016_09_05__14_46_21 | Simple and efficient reading/writing/modifying of complete files | URL |
| 936 | perl-file-slurp-tiny | 2016_09_05__14_52_01 | A simple, sane and efficient file slurper [discouraged] | URL |
| 937 | perl-file-slurper | 2016_09_05__14_41_29 | A simple, sane and efficient module to slurp a file | URL |
| 938 | perl-file-sort | 2017_01_30__12_45_49 | Sort a file or merge sort multiple files | URL |
| 939 | perl-file-spec | 2017_03_06__11_45_42 | None | URL |
| 940 | perl-file-which | 2016_09_05__14_58_40 | Perl implementation of the which utility as an api | URL |
| 941 | perl-filesys-df | 2016_09_07__08_57_39 | Perl extension for filesystem disk space information. | URL |
| 942 | perl-filter-simple | 2017_02_24__10_30_37 | None | URL |
| 943 | perl-findbin | 2017_02_24__10_35_06 | None | URL |
| 944 | perl-font-ttf | 2016_09_07__03_51_06 | Ttf font support for perl | URL |
| 945 | perl-forks | 2016_09_05__15_07_11 | Drop-in replacement for perl threads using fork() | URL |
| 946 | perl-gd | 2017_02_24__14_31_12 | Perl interface to the gd2 graphics library | URL |
| 947 | perl-gdgraph | 2016_09_07__12_25_38 | Produces charts with gd | URL |
| 948 | perl-gdtextutil | 2016_09_07__03_13_35 | Text utilities for use with gd | URL |
| 949 | perl-getopt-argvfile | 2017_03_07__08_03_39 | None | URL |
| 950 | perl-getopt-long | 2016_11_09__06_52_13 | Module to handle parsing command line options | URL |
| 951 | perl-git-wrapper | 2016_11_09__08_40_37 | Wrap git(7) command-line interface | URL |
| 952 | perl-git-wrapper-plus | 2016_11_09__08_41_42 | A toolkit for working with git::wrapper in an object oriented way. | URL |
| 953 | perl-graph | 2016_09_08__11_22_36 | A perl extension for keeping data partially sorted | URL |
| 954 | perl-graph-readwrite | 2016_12_03__08_55_56 | Write out directed graph in dot format | URL |
| 955 | perl-graphviz | 2016_09_05__15_16_32 | Interface to at&t's graphviz. deprecated. see graphviz2 | URL |
| 956 | perl-grass | 2016_09_20__13_51_33 | Gene Rearrangement AnalySiS: Takes pairs of coordinates describing potential rearrangement events and predicts the 'most interesting' fusion consequences that could occur. | URL |
| 957 | perl-hpc-runner | 2016_09_08__10_51_12 | Hpc runner::slurm, runner::mce and runner::threads base class | URL |
| 958 | perl-hpc-runner-command | 2017_03_12__11_55_35 | None | URL |
| 959 | perl-hpc-runner-mce | 2016_09_05__15_19_24 | Job submission using mce | URL |
| 960 | perl-hpc-runner-pbs | 2016_09_05__15_23_10 | Submit jobs to a pbs job scheduler. | URL |
| 961 | perl-hpc-runner-scheduler | 2016_09_05__15_27_54 | Base library for hpc::runner::slurm and hpc::runner::pbs | URL |
| 962 | perl-hpc-runner-slurm | 2016_09_05__15_37_33 | Submit bioinformatics hpc workflows with the slurm scheduler | URL |
| 963 | perl-html-element-extended | 2016_09_05__01_02_42 | Perl extension for manipulating a table composed of html::element style components. | URL |
| 964 | perl-html-entities-numbered | 2016_09_05__04_29_27 | Conversion of numbered html entities | URL |
| 965 | perl-html-formatter | 2016_09_05__15_45_56 | Base class for html formatters | URL |
| 966 | perl-html-parser | 2017_02_03__04_10_15 | Html parser class | URL |
| 967 | perl-html-tableextract | 2016_09_05__15_50_41 | Perl module for extracting the content contained in tables within an html document, either as text or encoded element trees. | URL |
| 968 | perl-html-tagset | 2017_01_30__12_46_31 | Data tables useful in parsing html | URL |
| 969 | perl-html-template | 2016_09_05__15_54_27 | Perl module to use html-like templating language | URL |
| 970 | perl-html-tidy | 2016_09_05__15_57_50 | (x)html validation in a perl object | URL |
| 971 | perl-html-tree | 2016_09_05__15_41_36 | Work with html in a dom-like tree structure | URL |
| 972 | perl-html-treebuilder-xpath | 2016_09_05__16_00_31 | Add xpath support to html::treebuilder | URL |
| 973 | perl-http-cookies | 2016_09_05__16_07_44 | Http cookie jars | URL |
| 974 | perl-http-daemon | 2016_09_05__16_11_35 | A simple http server class | URL |
| 975 | perl-http-date | 2017_02_03__04_12_24 | Date conversion routines | URL |
| 976 | perl-http-message | 2016_09_05__16_05_14 | Http style messages | URL |
| 977 | perl-http-negotiate | 2016_09_05__16_21_50 | Choose a variant to serve | URL |
| 978 | perl-image-exiftool | 2017_03_17__08_13_38 | None | URL |
| 979 | perl-image-info | 2016_09_07__08_22_44 | Extract meta information from image files | URL |
| 980 | perl-image-size | 2016_09_05__16_25_15 | A library to extract height/width from images | URL |
| 981 | perl-inline | 2016_11_08__07_15_48 | Write perl subroutines in other programming languages | URL |
| 982 | perl-inline-c | 2016_11_08__07_14_24 | A library to extract height/width from images | URL |
| 983 | perl-integer | 2017_02_24__10_27_22 | None | URL |
| 984 | perl-io-all | 2016_11_08__07_18_25 | Combines all of the best perl io modules into a single nifty object oriented interface | URL |
| 985 | perl-io-compress | 2016_11_09__08_42_26 | Io interface to compressed data files/buffers | URL |
| 986 | perl-io-compress-deflate | 2017_02_24__10_29_05 | None | URL |
| 987 | perl-io-handle | 2017_02_23__09_03_25 | None | URL |
| 988 | perl-io-html | 2017_02_03__04_10_56 | Open an html file with automatic charset detection | URL |
| 989 | perl-io-interactive | 2016_08_31__13_09_52 | Utilities for interactive i/o | URL |
| 990 | perl-io-prompt | 2017_02_09__07_56_23 | None | URL |
| 991 | perl-io-scalar | 2017_02_24__10_34_39 | None | URL |
| 992 | perl-io-sessiondata | 2016_09_05__16_38_05 | Supporting module for soap::lite | URL |
| 993 | perl-io-socket-inet6 | 2016_09_07__22_04_36 | Object interface for af_inet/af_inet6 domain sockets | URL |
| 994 | perl-io-socket-ssl | 2016_09_08__09_53_57 | Nearly transparent ssl encapsulation for io::socket::inet. | URL |
| 995 | perl-io-string | 2017_02_24__10_38_05 | Emulate file interface for in-core strings | URL |
| 996 | perl-io-stringy | 2016_09_05__16_28_06 | Write a file which is updated atomically | URL |
| 997 | perl-io-tty | 2016_09_05__16_34_07 | Pseudo ttys and constants | URL |
| 998 | perl-io-uncompress-bunzip2 | 2017_02_24__10_34_16 | None | URL |
| 999 | perl-io-uncompress-gunzip | 2017_02_24__10_28_39 | None | URL |
| 1000 | perl-io-uncompress-rawinflate | 2017_02_24__10_36_58 | None | URL |
| 1001 | perl-io-zlib | 2016_11_09__08_43_08 | Io:: style interface to compress::zlib | URL |
| 1002 | perl-ipc-system-simple | 2016_09_07__13_02_36 | Run commands simply, with detailed diagnostics | URL |
| 1003 | perl-jcode | 2016_09_07__12_49_52 | Japanese charset handler | URL |
| 1004 | perl-json | 2017_01_10__08_09_44 | Json (javascript object notation) encoder/decoder | URL |
| 1005 | perl-json-maybexs | 2017_01_05__07_53_12 | Use cpanel::json::xs with a fallback to json::xs and json::pp | URL |
| 1006 | perl-json-xs | 2016_09_07__09_46_24 | Json serialising/deserialising, done correctly and fast | URL |
| 1007 | perl-libwww-perl | 2016_09_07__05_29_25 | The world-wide web library for perl | URL |
| 1008 | perl-libxml-perl | 2016_09_07__16_13_27 | Perl sax parser using nsgmls | URL |
| 1009 | perl-list-compare | 2017_03_15__08_09_23 | None | URL |
| 1010 | perl-list-moreutils | 2016_09_08__06_02_38 | Provide the stuff missing in list::util | URL |
| 1011 | perl-list-someutils | 2017_03_04__08_12_04 | None | URL |
| 1012 | perl-list-uniq | 2016_11_09__06_54_40 | Extract the unique elements of a list | URL |
| 1013 | perl-list-util | 2017_02_24__10_26_32 | None | URL |
| 1014 | perl-locale | 2017_02_24__10_39_13 | None | URL |
| 1015 | perl-locale-maketext-simple | 2017_02_24__10_36_11 | None | URL |
| 1016 | perl-log-any | 2017_01_05__07_54_02 | Bringing loggers and listeners together | URL |
| 1017 | perl-log-log4perl | 2016_10_09__21_02_12 | Log4j implementation for perl | URL |
| 1018 | perl-lwp-mediatypes | 2016_09_05__17_44_16 | Guess media type for a file or a url | URL |
| 1019 | perl-lwp-protocol-https | 2017_04_11__17_59_35 | Provide https support for lwp::useragent | URL |
| 1020 | perl-lwp-simple | 2016_09_07__09_33_50 | Simple procedural interface to lwp | URL |
| 1021 | perl-mailtools | 2016_09_05__17_48_42 | Various e-mail related modules | URL |
| 1022 | perl-math-bezier | 2016_09_08__03_04_43 | Solution of bezier curves | URL |
| 1023 | perl-math-cdf | 2016_09_05__17_52_33 | Generate probabilities and quantiles from several statistical probability functions | URL |
| 1024 | perl-math-combinatorics | 2016_12_03__08_55_36 | Perform combinations and permutations on lists | URL |
| 1025 | perl-math-derivative | 2016_09_07__18_55_43 | Numeric 1st and 2nd order differentiation. | URL |
| 1026 | perl-math-random | 2016_09_05__17_54_45 | Random number generators | URL |
| 1027 | perl-math-round | 2016_09_05__17_57_15 | Perl extension for rounding numbers | URL |
| 1028 | perl-math-spline | 2016_09_05__17_59_30 | Cubic spline interpolation of data | URL |
| 1029 | perl-math-vecstat | 2016_09_08__01_45_15 | Some basic numeric stats on vectors | URL |
| 1030 | perl-mce | 2017_03_04__08_12_39 | None | URL |
| 1031 | perl-memoize | 2016_11_09__08_43_45 | Make functions faster by trading space for time | URL |
| 1032 | perl-mime-lite | 2016_09_05__18_05_25 | Handy-dandy mime mailing class | URL |
| 1033 | perl-mime-quotedprint | 2017_02_23__09_04_06 | None | URL |
| 1034 | perl-mime-tools | 2016_09_05__18_01_40 | Tools to manipulate mime messages | URL |
| 1035 | perl-mime-types | 2016_09_08__10_11_16 | Definition of mime types | URL |
| 1036 | perl-mixin-linewise | 2016_08_31__13_11_32 | Write your linewise code for handles; this does the rest | URL |
| 1037 | perl-mldbm | 2016_09_05__18_07_14 | Store multi-level perl hash structure in single level tied hash | URL |
| 1038 | perl-mldbm-sync | 2016_09_07__06_38_14 | Safe concurrent access to mldbm databases | URL |
| 1039 | perl-module-build | 2017_02_03__04_09_51 | Build and install perl modules | URL |
| 1040 | perl-module-build-tiny | 2016_09_05__18_10_14 | A tiny replacement for module::build | URL |
| 1041 | perl-module-implementation | 2016_09_07__23_28_39 | Loads one of several alternate underlying implementations for a module | URL |
| 1042 | perl-module-load | 2017_02_24__10_40_35 | None | URL |
| 1043 | perl-module-load-conditional | 2017_02_24__10_24_56 | None | URL |
| 1044 | perl-module-runtime | 2016_09_07__09_36_12 | Runtime module handling | URL |
| 1045 | perl-module-scandeps | 2017_03_07__08_04_22 | None | URL |
| 1046 | perl-moo | 2017_01_10__08_10_02 | Minimalist object orientation (with moose compatibility) | URL |
| 1047 | perl-moosex-app | 2016_11_09__08_44_42 | Write user-friendly command line apps with even less suffering | URL |
| 1048 | perl-moosex-app-role-log4perl | 2016_11_09__06_56_11 | Add basic log::log4perl logging to a moosex::app application as a role. | URL |
| 1049 | perl-moosex-fileattribute | 2016_08_31__13_12_53 | Sugar for classes that have file or directory attributes | URL |
| 1050 | perl-moosex-getopt | 2016_08_31__13_13_31 | A moose role for processing command line options | URL |
| 1051 | perl-moosex-types | 2016_08_31__13_14_08 | Organise your moose types in libraries | URL |
| 1052 | perl-moosex-types-path-class | 2016_08_31__13_14_50 | A path::class type library for moose | URL |
| 1053 | perl-mozilla-ca | 2016_09_05__18_19_59 | Mozilla's ca cert bundle in pem format | URL |
| 1054 | perl-namespace-autoclean | 2017_03_04__08_13_19 | None | URL |
| 1055 | perl-namespace-clean | 2017_03_04__08_14_02 | None | URL |
| 1056 | perl-net-ftp | 2017_02_24__10_42_11 | None | URL |
| 1057 | perl-net-http | 2016_09_05__04_54_11 | Low-level http connection (client) | URL |
| 1058 | perl-net-netrc | 2017_02_24__10_29_27 | None | URL |
| 1059 | perl-net-ssleay | 2016_09_05__21_14_42 | Perl extension for using openssl | URL |
| 1060 | perl-ntlm | 2016_09_08__08_20_46 | An ntlm authentication module | URL |
| 1061 | perl-number-compare | 2017_03_30__08_30_54 | Numeric comparisons | URL |
| 1062 | perl-number-format | 2016_09_05__21_17_19 | Perl extension for formatting numbers | URL |
| 1063 | perl-ole-storage_lite | 2016_09_05__21_19_56 | Read and write ole storage files. | URL |
| 1064 | perl-onto-perl | 2016_12_20__07_25_33 | Perl modules for manipulating obo-formatted ontologies, such as the gene ontology (go) | URL |
| 1065 | perl-package-stash | 2017_01_19__10_36_11 | Routines for manipulating stashes | URL |
| 1066 | perl-par | 2017_03_07__08_05_09 | None | URL |
| 1067 | perl-par-dist | 2017_03_07__08_06_03 | None | URL |
| 1068 | perl-par-packer | 2017_03_08__01_52_21 | None | URL |
| 1069 | perl-parallel-forkmanager | 2016_09_05__21_22_41 | A simple parallel processing fork manager | URL |
| 1070 | perl-params-check | 2017_02_24__10_36_33 | None | URL |
| 1071 | perl-params-util | 2016_11_09__06_56_51 | Simple, compact and correct param-checking functions | URL |
| 1072 | perl-params-validationcompiler | 2017_03_04__16_54_00 | None | URL |
| 1073 | perl-parse-recdescent | 2016_09_05__21_31_10 | Generate recursive-descent parsers | URL |
| 1074 | perl-parse-yapp | 2016_10_30__11_37_08 | Perl extension for generating and using lalr parsers. | URL |
| 1075 | perl-path-class | 2016_09_05__21_34_28 | Cross-platform path specification manipulation | URL |
| 1076 | perl-path-tiny | 2016_09_05__21_36_47 | File path utility | URL |
| 1077 | perl-pathtools | 2016_09_07__20_21_12 | Get pathname of current working directory | URL |
| 1078 | perl-pbkdf2-tiny | 2016_09_07__11_16_12 | Minimalist pbkdf2 (rfc 2898) with hmac-sha1 or hmac-sha2 | URL |
| 1079 | perl-pcap | 2016_10_03__16_03_21 | Ngs reference implementations and helper code for the igcg/tcga pan-cancer analysis project | URL |
| 1080 | perl-pdf-api2 | 2016_09_05__21_40_58 | Facilitates the creation and modification of pdf files | URL |
| 1081 | perl-pegex | 2016_11_08__07_19_40 | Pegex grammar for the pegex grammar language | URL |
| 1082 | perl-perl-osnames | 2017_01_05__07_54_45 | List possible $^o ($osname) values, with description | URL |
| 1083 | perl-perl-unsafe-signals | 2016_09_05__21_46_22 | Allow unsafe handling of signals in selected blocks | URL |
| 1084 | perl-perl-version | 2016_11_09__08_45_25 | Parse and manipulate perl version strings | URL |
| 1085 | perl-perlio | 2017_02_24__10_40_58 | None | URL |
| 1086 | perl-perlio-encoding | 2017_02_24__10_41_47 | None | URL |
| 1087 | perl-perlio-gzip | 2016_09_05__21_43_52 | Perlio interface to gzip/gunzip | URL |
| 1088 | perl-pod-checker | 2017_02_24__10_33_27 | None | URL |
| 1089 | perl-pod-elemental | 2016_08_31__13_15_31 | Work with nestable pod elements | URL |
| 1090 | perl-pod-plaintext | 2017_02_24__10_28_16 | None | URL |
| 1091 | perl-pod-simple-text | 2017_02_23__09_05_24 | None | URL |
| 1092 | perl-posix | 2017_02_24__10_33_51 | None | URL |
| 1093 | perl-postscript | 2016_09_05__21_49_48 | Helper module for postscript::textblock | URL |
| 1094 | perl-proc-fork | 2016_09_08__01_25_17 | Simple, intuitive interface to the fork() system call | URL |
| 1095 | perl-readonly | 2016_09_07__09_38_10 | Facility for creating read-only scalars, arrays, hashes | URL |
| 1096 | perl-regexp-common | 2016_09_05__21_52_49 | Provide commonly requested regular expressions | URL |
| 1097 | perl-role-tiny | 2016_09_05__21_55_19 | Roles. like a nouvelle cuisine portion size slice of moose. | URL |
| 1098 | perl-role-tiny-with | 2017_02_24__10_27_48 | None | URL |
| 1099 | perl-safe | 2017_02_24__10_32_14 | None | URL |
| 1100 | perl-sanger-cgp-allelecount | 2016_09_05__21_58_26 | Support code for ngs copy number algorithm | URL |
| 1101 | perl-sanger-cgp-battenberg | 2016_09_07__04_35_21 | Detect subclonality and copy number in matched ngs data | URL |
| 1102 | perl-sanger-cgp-vagrent | 2016_12_03__08_57_36 | A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences | URL |
| 1103 | perl-sanger-cgp-vcf | 2016_09_05__22_01_49 | A set of common perl utilities for generating consistent vcf headers | URL |
| 1104 | perl-scalar-list-utils | 2016_10_09__15_19_14 | Common scalar and list utility subroutines | URL |
| 1105 | perl-scalar-util-numeric | 2016_09_05__22_04_09 | Numeric tests for perl scalars | URL |
| 1106 | perl-scope-guard | 2016_10_31__21_43_03 | Lexically-scoped resource management | URL |
| 1107 | perl-set-intspan | 2016_09_05__22_08_33 | Manages sets of integers, newsrc style | URL |
| 1108 | perl-set-scalar | 2016_09_05__22_10_57 | Basic set operations | URL |
| 1109 | perl-soap-lite | 2016_09_07__19_03_58 | Perl's web services toolkit | URL |
| 1110 | perl-socket6 | 2016_09_05__22_14_05 | Ipv6 related part of the c socket.h defines and structure manipulators | URL |
| 1111 | perl-sort-naturally | 2016_09_05__22_16_46 | Sort lexically, but sort numeral parts numerically | URL |
| 1112 | perl-sort-versions | 2016_11_09__06_58_18 | A perl 5 module for sorting of revision-like numbers | URL |
| 1113 | perl-specio-exporter | 2017_03_04__16_53_40 | None | URL |
| 1114 | perl-spiffy | 2016_09_05__22_19_40 | Spiffy perl interface framework for you | URL |
| 1115 | perl-spreadsheet-parseexcel | 2016_09_05__22_21_44 | Read information from an excel file. | URL |
| 1116 | perl-spreadsheet-writeexcel | 2016_09_08__03_18_08 | Write to a cross platform excel binary file | URL |
| 1117 | perl-sql-statement | 2016_09_05__22_28_21 | Sql parsing and processing engine | URL |
| 1118 | perl-statistics-basic | 2016_09_05__22_31_57 | URL | |
| 1119 | perl-statistics-descriptive | 2016_09_05__22_36_50 | Module of basic descriptive statistical functions | URL |
| 1120 | perl-statistics-distributions | 2016_09_05__22_39_35 | Perl module for calculating critical values and upper probabilities of common statistical distributions | URL |
| 1121 | perl-statistics-frequency | 2016_11_09__08_46_02 | Simple counting of elements | URL |
| 1122 | perl-statistics-lite | 2016_09_05__22_41_44 | Small stats stuff. | URL |
| 1123 | perl-statistics-ttest | 2016_09_05__22_44_57 | Perl module to perform t-test on 2 independent samples statistics::ttest::sufficient - perl module to perfrom t-test on 2 indepdent samples using sufficient statistics | URL |
| 1124 | perl-string-approx | 2017_03_04__08_14_37 | None | URL |
| 1125 | perl-sub-attribute | 2017_03_04__08_15_12 | None | URL |
| 1126 | perl-sub-exporter | 2016_11_09__08_46_38 | A sophisticated exporter for custom-built routines | URL |
| 1127 | perl-sub-exporter-progressive | 2016_09_05__22_47_16 | Only use sub::exporter if you need it | URL |
| 1128 | perl-sub-identify | 2017_02_24__21_27_19 | None | URL |
| 1129 | perl-sub-install | 2016_11_09__08_47_16 | Install subroutines into packages easily | URL |
| 1130 | perl-sub-name | 2017_03_15__08_10_22 | None | URL |
| 1131 | perl-sub-uplevel | 2016_09_05__22_50_42 | Apparently run a function in a higher stack frame | URL |
| 1132 | perl-svg | 2016_09_05__01_15_39 | Perl extension for generating scalable vector graphics (svg) documents | URL |
| 1133 | perl-svg-graph | 2016_09_08__10_51_56 | Visualize your data in scalable vector graphics (svg) format. | URL |
| 1134 | perl-symbol | 2017_02_23__09_03_04 | None | URL |
| 1135 | perl-symbol-util | 2017_03_04__16_54_20 | None | URL |
| 1136 | perl-tap-harness-env | 2017_02_24__10_35_49 | None | URL |
| 1137 | perl-task-weaken | 2016_09_05__18_35_43 | Ensure that a platform has weaken support | URL |
| 1138 | perl-template-toolkit | 2016_09_06__23_03_10 | Comprehensive template processing system | URL |
| 1139 | perl-term-app-roles | 2017_01_05__07_55_34 | Collection of roles for terminal-based application | URL |
| 1140 | perl-term-detect-software | 2017_01_05__07_56_16 | Detect terminal (emulator) software and its capabilities | URL |
| 1141 | perl-term-encoding | 2017_02_24__10_38_49 | Detect encoding of the current terminal | URL |
| 1142 | perl-termreadkey | 2016_09_05__18_38_05 | A perl module for simple terminal control | URL |
| 1143 | perl-test-class-moose | 2017_03_05__08_08_13 | None | URL |
| 1144 | perl-test-classapi | 2016_11_08__07_20_22 | Provides basic first-pass api testing for large class trees | URL |
| 1145 | perl-test-cpan-meta | 2016_09_05__18_40_23 | Validate your cpan meta.json files | URL |
| 1146 | perl-test-deep | 2016_09_08__10_17_20 | Extremely flexible deep comparison | URL |
| 1147 | perl-test-differences | 2016_09_08__09_38_19 | Test strings and data structures and show differences if not ok | URL |
| 1148 | perl-test-eol | 2016_09_05__18_43_27 | Check the correct line endings in your project | URL |
| 1149 | perl-test-exception | 2016_09_07__15_39_53 | Test exception-based code | URL |
| 1150 | perl-test-fatal | 2016_09_05__18_45_22 | Incredibly simple helpers for testing code with exceptions | URL |
| 1151 | perl-test-files | 2016_12_30__07_26_27 | A test::builder based module to ease testing with files and dirs | URL |
| 1152 | perl-test-harness | 2017_02_24__10_39_38 | Run perl standard test scripts with statistics | URL |
| 1153 | perl-test-inter | 2016_12_20__07_26_16 | Framework for more readable interactive test scripts | URL |
| 1154 | perl-test-leaktrace | 2016_09_07__09_14_30 | Traces memory leaks | URL |
| 1155 | perl-test-more | 2017_02_24__10_25_21 | None | URL |
| 1156 | perl-test-most | 2016_09_05__18_47_23 | Most commonly needed test functions and features | URL |
| 1157 | perl-test-notabs | 2016_09_05__18_49_43 | Check the presence of tabs in your project | URL |
| 1158 | perl-test-nowarnings | 2016_09_07__22_45_53 | Make sure you didn't emit any warnings while testing | URL |
| 1159 | perl-test-output | 2017_01_01__07_27_19 | Utilities to test stdout and stderr messages. | URL |
| 1160 | perl-test-pod | 2016_09_05__18_51_44 | Check for pod errors in files | URL |
| 1161 | perl-test-requires | 2016_09_05__18_53_38 | Checks to see if the module can be loaded | URL |
| 1162 | perl-test-simple | 2017_03_14__13_43_57 | Basic utilities for writing tests. | URL |
| 1163 | perl-test-unit-lite | 2017_02_24__10_38_27 | None | URL |
| 1164 | perl-test-warn | 2016_09_05__18_59_41 | Perl extension to test methods for warnings | URL |
| 1165 | perl-test-warnings | 2016_09_05__18_57_35 | Test for warnings and the lack of them | URL |
| 1166 | perl-test-xml | 2016_09_07__16_15_57 | Compare xml in perl tests | URL |
| 1167 | perl-test-yaml | 2017_04_11__17_59_35 | Testing module for yaml implementations | URL |
| 1168 | perl-test2 | 2017_03_04__08_15_45 | None | URL |
| 1169 | perl-text-ansitable | 2017_03_05__08_09_09 | None | URL |
| 1170 | perl-text-asciitable | 2017_03_05__08_33_10 | None | URL |
| 1171 | perl-text-csv | 2016_11_02__21_37_17 | Comma-separated values manipulator (using xs or pureperl) | URL |
| 1172 | perl-text-diff | 2016_09_05__19_01_55 | Perform diffs on files and record sets | URL |
| 1173 | perl-text-format | 2016_09_05__19_03_43 | Format text | URL |
| 1174 | perl-text-glob | 2017_03_30__08_31_11 | Match globbing patterns against text | URL |
| 1175 | perl-text-nsp | 2016_09_07__15_03_33 | Extract collocations and ngrams from text | URL |
| 1176 | perl-text-parsewords | 2017_03_03__12_34_36 | Parse text into an array of tokens or array of arrays | URL |
| 1177 | perl-text-soundex | 2016_09_05__19_08_47 | Implementation of the soundex algorithm. | URL |
| 1178 | perl-text-tabs | 2017_02_24__10_24_10 | None | URL |
| 1179 | perl-text-tabs-wrap | 2016_10_27__07_09_15 | Expand tabs and do simple line wrapping | URL |
| 1180 | perl-text-template | 2017_03_15__08_11_51 | None | URL |
| 1181 | perl-text-wrap | 2017_02_24__10_33_01 | None | URL |
| 1182 | perl-threaded | 2017_01_12__10_10_31 | The perl language. | URL |
| 1183 | perl-tie-cache | 2016_09_05__19_10_54 | Lru cache in memory | URL |
| 1184 | perl-tie-cacher | 2016_12_20__07_27_22 | Cache a (sub)set of key/value pairs. tie and oo interface. | URL |
| 1185 | perl-tie-hash | 2017_02_23__09_01_54 | None | URL |
| 1186 | perl-tie-hash-indexed | 2017_03_29__08_13_28 | None | URL |
| 1187 | perl-tie-ixhash | 2016_09_05__19_12_55 | Ordered associative arrays for perl | URL |
| 1188 | perl-time-hires | 2017_02_24__21_26_12 | High resolution alarm, sleep, gettimeofday, interval timers | URL |
| 1189 | perl-time-local | 2017_02_24__10_26_59 | None | URL |
| 1190 | perl-time-piece | 2017_02_24__10_31_00 | None | URL |
| 1191 | perl-timedate | 2016_09_07__06_35_43 | Date formating subroutines | URL |
| 1192 | perl-tree-dag_node | 2016_09_05__19_17_47 | An n-ary tree | URL |
| 1193 | perl-try-tiny | 2017_03_03__12_33_55 | Minimal try/catch with proper preservation of $@ | URL |
| 1194 | perl-type-tiny | 2016_09_05__19_21_42 | Tiny, yet moo(se)-compatible type constraint | URL |
| 1195 | perl-types-serialiser | 2016_09_04__21_02_29 | Simple data types for common serialisation formats | URL |
| 1196 | perl-unicode-map | 2016_09_05__21_17_40 | Map charsets from and to utf-16 unicode | URL |
| 1197 | perl-unicode-normalize | 2017_02_24__10_23_44 | None | URL |
| 1198 | perl-unicode-stringprep | 2016_09_07__08_25_11 | Preparation of internationalized strings (rfc 3454) | URL |
| 1199 | perl-uri | 2016_09_05__21_21_41 | Uniform resource identifiers (absolute and relative) | URL |
| 1200 | perl-variable-magic | 2017_03_04__08_16_20 | None | URL |
| 1201 | perl-vars | 2017_02_24__10_29_47 | None | URL |
| 1202 | perl-vcftools-vcf | 2016_09_05__21_24_53 | Cpanm ready distribution of vcftools perl libraries | URL |
| 1203 | perl-velvetoptimiser | 2016_09_06__10_03_14 | Automatically optimise three of velvet's assembly parameters. | URL |
| 1204 | perl-version-next | 2016_11_09__08_49_31 | Increment module version numbers simply and correctly | URL |
| 1205 | perl-want | 2017_02_03__11_58_33 | "this module generalises the mechanism of the wantarray function, allowing a function | URL |
| 1206 | perl-warnings-register | 2017_02_23__09_02_16 | None | URL |
| 1207 | perl-www-robotrules | 2016_09_05__21_29_00 | Database of robots.txt-derived permissions | URL |
| 1208 | perl-xml-dom | 2016_09_05__21_33_02 | A perl module for building dom level 1 compliant document structures | URL |
| 1209 | perl-xml-dom-xpath | 2016_09_05__21_36_55 | Perl extension to add xpath support to xml::dom, using xml::xpath engine | URL |
| 1210 | perl-xml-filter-buffertext | 2016_09_05__21_40_05 | Filter to put all characters() in one event | URL |
| 1211 | perl-xml-libxml | 2017_04_11__17_59_35 | Interface to gnome libxml2 xml parsing and dom library | URL |
| 1212 | perl-xml-libxslt | 2017_04_11__17_59_35 | Interface to gnome libxslt library | URL |
| 1213 | perl-xml-namespacesupport | 2016_09_05__21_46_24 | A simple generic namespace support class | URL |
| 1214 | perl-xml-parser | 2016_09_05__21_52_09 | A perl module for parsing xml documents | URL |
| 1215 | perl-xml-regexp | 2016_09_04__21_54_23 | Regular expressions for xml tokens | URL |
| 1216 | perl-xml-sax | 2016_09_05__22_01_25 | Simple api for xml | URL |
| 1217 | perl-xml-sax-base | 2016_09_05__21_54_36 | Base class for sax drivers and filters | URL |
| 1218 | perl-xml-sax-expat | 2016_09_05__21_58_09 | Sax driver for expat | URL |
| 1219 | perl-xml-sax-writer | 2016_09_05__22_03_45 | Sax2 xml writer | URL |
| 1220 | perl-xml-semanticdiff | 2016_09_05__22_07_28 | Perl extension for comparing xml documents. | URL |
| 1221 | perl-xml-simple | 2016_09_05__22_11_11 | An api for simple xml files | URL |
| 1222 | perl-xml-twig | 2016_09_09__22_58_40 | Xml, the perl way | URL |
| 1223 | perl-xml-writer | 2016_09_05__22_13_39 | Easily generate well-formed, namespace-aware xml. | URL |
| 1224 | perl-xml-xpath | 2016_09_05__21_28_47 | Parse and evaluate xpath statements. | URL |
| 1225 | perl-xml-xpathengine | 2016_09_05__21_40_22 | A re-usable xpath engine for dom-like trees | URL |
| 1226 | perl-xsloader | 2017_02_24__10_31_22 | 'dynamically load c libraries into perl code' | URL |
| 1227 | perl-yaml | 2016_09_07__05_07_45 | Yaml ain't markup language | URL |
| 1228 | perl-yaml-libyaml | 2016_11_08__07_21_04 | Perl yaml serialization using xs and libyaml | URL |
| 1229 | pgma-simple | 2016_12_08__07_14_19 | Pgma is a simple program for building wpgma trees. | URL |
| 1230 | phonenumbers | 2016_09_06__03_39_34 | Python version of google's common library for parsing, formatting, storing and validating international phone numbers. | URL |
| 1231 | phylip | 2017_03_24__18_29_34 | None | URL |
| 1232 | phylotoast | 2016_09_06__23_11_45 | Useful additions to the qiime analysis pipeline including tools for data visualization and cluster-computing. | URL |
| 1233 | phylowgs | 2016_09_07__19_18_42 | Application for inferring subclonal composition and evolution from whole-genome sequencing data | URL |
| 1234 | picard | 2016_11_19__17_53_16 | Java tools for working with ngs data in the bam format | URL |
| 1235 | picopore | 2017_03_30__09_18_41 | None | URL |
| 1236 | picrust | 2016_11_27__22_33_12 | 'picrust: phylogenetic investigation of communities by reconstruction of unobserved states' | URL |
| 1237 | pileometh | 2016_09_14__07_22_29 | A (mostly) universal methylation extractor for bs-seq experiments. | URL |
| 1238 | piler | 2016_09_05__22_15_46 | Piler is public domain software for analyzing repetitive dna found in genome sequences. | URL |
| 1239 | pilon | 2017_03_24__01_08_19 | pilon is an automated genome assembly improvement and variant detection tool. | URL |
| 1240 | pipmir | 2016_11_16__21_35_13 | We developed the pipmir algorithm to identify novel plant mirna genes from a combination of deep sequencing data and genomic features. | URL |
| 1241 | piranha | 2016_06_09__22_18_33 | Piranha is a peak-caller for clip- and rip-seq data. | URL |
| 1242 | planemo | 2017_02_07__06_16_43 | Command-line utilities to assist in building tools for the galaxy project (http://galaxyproject.org/). | URL |
| 1243 | plant_tribes_assembly_post_processor | 2016_11_23__00_27_17 | Transcriptome assembly post processing pipeline | URL |
| 1244 | plant_tribes_gene_family_classifier | 2017_01_28__08_01_39 | Gene family classification pipeline | URL |
| 1245 | plant_tribes_phylogenomics_analysis | 2017_02_11__07_54_37 | None | URL |
| 1246 | plastid | 2017_03_15__22_44_49 | None | URL |
| 1247 | platypus-conquistador | 2016_09_10__06_26_09 | Platypus conquistador: confirming specific taxonomic groups within your metagenomic samples. | URL |
| 1248 | platypus-variant | 2016_09_05__22_28_36 | A haplotype-based variant caller for next generation sequence data | URL |
| 1249 | poa | 2016_09_05__22_41_40 | Poa is partial order alignment, a fast program for multiple sequence alignment in bioinformatics. its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. | URL |
| 1250 | pomegranate | 2017_04_11__17_59_35 | Pomegranate is a graphical models library for python, implemented in cython for speed. | URL |
| 1251 | popt | 2017_03_10__22_17_24 | None | URL |
| 1252 | poretools | 2017_02_16__07_20_37 | Poretools: a toolkit for working with nanopore sequencing data from oxford nanopore | URL |
| 1253 | postgresql | 2016_05_03__06_00_20 | A sophisticated object-relational DBMS | URL |
| 1254 | potrace | 2017_04_11__17_59_35 | A tool for tracing a bitmap, which means, transforming a bitmap into a smooth, scalable image | URL |
| 1255 | pout2mzid | 2017_03_02__08_02_29 | None | URL |
| 1256 | pp | 2017_02_04__08_05_57 | Parallel and distributed programming for python | URL |
| 1257 | ppanini | 2016_11_27__22_58_44 | 'ppanini: prioritization and prediction of functional annotations for novel and important genes via automated data network integration.' | URL |
| 1258 | prank | 2016_09_05__22_55_48 | Prank is a probabilistic multiple alignment program for dna, codon and amino-acid sequences. | URL |
| 1259 | preseq | 2016_09_05__23_01_39 | Software for predicting library complexity and genome coverage in high-throughput sequencing | URL |
| 1260 | primer3-py | 2017_03_10__08_04_53 | None | URL |
| 1261 | primerprospector | 2017_01_15__19_18_25 | "primer prospector is a pipeline of programs to design and analyze pcr primers." | URL |
| 1262 | probamconvert | 2017_03_17__11_02_41 | None | URL |
| 1263 | prodigal | 2017_01_17__01_18_22 | Prodigal (prokaryotic dynamic programming genefinding algorithm) is a microbial (bacterial and archaeal) gene finding program developed at oak ridge national laboratory and the university of tennessee. | URL |
| 1264 | prokka | 2017_03_17__09_52_52 | A tool for the rapid annotation of prokaryotic genomes | URL |
| 1265 | pronto | 2016_09_07__20_36_14 | Python frontend to ontologies - a library to parse, create, browse and export ontologies. | URL |
| 1266 | prosic | 2017_03_28__19_48_44 | A caller for somatic insertions and deletions. | URL |
| 1267 | proteowizard | 2016_09_29__20_33_57 | tools for dealing with mass spectrometry files (e.g., mzml, mzxml, mzidentml, mgf) | URL |
| 1268 | protrac | 2017_04_11__17_59_35 | Pirna detection | URL |
| 1269 | pullseq | 2017_03_11__08_05_17 | None | URL |
| 1270 | py-graphviz | 2016_09_06__20_45_47 | Simple python interface for graphviz | URL |
| 1271 | py2bit | 2017_01_21__23_18_16 | A package for accessing 2bit files using lib2bit | URL |
| 1272 | py2neo | 2017_03_11__08_06_28 | None | URL |
| 1273 | pyalveo | 2016_10_12__18_16_22 | A python library for interfacing with the alveo api | URL |
| 1274 | pyaml | 2016_09_06__04_23_35 | Pyyaml-based module to produce pretty and readable yaml-serialized data | URL |
| 1275 | pyani | 2016_11_23__09_51_40 | 'pyani provides a package and script for calculation of genome-scale average nucleotide identity.' | URL |
| 1276 | pyasn1-modules | 2016_09_06__04_28_55 | A small but growing collection of asn.1 data structures expressed in python terms using pyasn1 data model | URL |
| 1277 | pybedtools | 2017_01_26__15_08_05 | Wraps bedtools for use in python and adds many additional features. | URL |
| 1278 | pybel | 2017_03_10__22_20_14 | None | URL |
| 1279 | pybigwig | 2017_03_30__08_17_37 | A python extension written in c for quick access to bigwig files. | URL |
| 1280 | pycli | 2016_09_07__11_53_06 | Simple, object-oriented approach to python cli apps | URL |
| 1281 | pycluster | 2016_09_07__05_49_42 | Clustering module for python | URL |
| 1282 | pycodestyle | 2016_09_05__21_44_19 | Python style guide checker | URL |
| 1283 | pycsg | 2016_09_07__11_53_59 | Python port of csg.js from evan wallace | URL |
| 1284 | pydoe | 2016_09_07__12_14_01 | Design of experiments for python | URL |
| 1285 | pyfaidx | 2017_01_18__20_04_25 | Pyfaidx: efficient pythonic random access to fasta subsequences | URL |
| 1286 | pyfasta | 2017_04_11__17_59_35 | Fast, memory-efficient, pythonic (and command-line) access to fasta sequence files | URL |
| 1287 | pyfastaq | 2016_09_21__18_27_00 | Script to manipulate fasta and fastq files, plus api for developers | URL |
| 1288 | pyfiglet | 2017_03_11__08_08_41 | None | URL |
| 1289 | pygresql | 2016_09_03__13_06_10 | Python postgresql interfaces | URL |
| 1290 | pyhashxx | 2016_11_18__07_15_03 | Python wrapper for xxhash algorithm | URL |
| 1291 | pyinotify | 2016_09_07__07_31_30 | Linux filesystem events monitoring | URL |
| 1292 | pylibseq | 2016_11_02__21_39_12 | A python interface to libsequence | URL |
| 1293 | pyliftover | 2016_12_05__08_17_24 | Pure-python implementation of ucsc ``liftover`` genome coordinate conversion. | URL |
| 1294 | pyloh | 2016_09_05__14_24_54 | Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity | URL |
| 1295 | pymot | 2017_03_18__11_39_05 | None | URL |
| 1296 | pymummer | 2016_12_15__07_37_18 | Wrapper for mummer | URL |
| 1297 | pynacl | 2016_09_05__15_00_01 | Python binding to the networking and cryptography (nacl) library | URL |
| 1298 | pynast | 2016_09_07__09_01_26 | The python nearest alignment space termination tool | URL |
| 1299 | pyomo | 2016_09_07__02_06_30 | Pyomo: python optimization modeling objects | URL |
| 1300 | pypeflow | 2017_01_05__16_58_46 | "light weight and reusable make / flow data process library written in python" | URL |
| 1301 | pypore | 2017_02_12__23_25_25 | Pythonic/cythonic nanopore translocation analysis | URL |
| 1302 | pyprophet | 2017_04_11__17_59_35 | Python reimplementation of mprophet peak scoring | URL |
| 1303 | pyqi | 2016_09_09__17_38_03 | Pyqi: expose your interface | URL |
| 1304 | pyquant-ms | 2017_04_11__17_59_35 | A framework for the analysis of quantitative mass spectrometry data | URL |
| 1305 | pyrad | 2016_05_13__12_45_54 | Assembly and analysis of radseq data sets | URL |
| 1306 | pysam | 2017_03_22__09_51_07 | Pysam is a python module for reading and manipulating samfiles. it is a lightweight wrapper of the samtools c-api. pysam also includes an interface for tabix. | URL |
| 1307 | pysamstats | 2017_01_24__11_46_56 | A python utility for calculating statistics against genome position based on sequence alignments from a sam, bam or cram file. | URL |
| 1308 | pyscaf | 2017_02_13__07_58_39 | None | URL |
| 1309 | pysftp | 2017_02_28__06_13_14 | A friendly face on sftp | URL |
| 1310 | pytabix | 2016_09_06__00_48_48 | Fast random access to sorted files compressed with bgzip and indexed by tabix | URL |
| 1311 | pytest-cov | 2016_12_07__12_44_10 | Pytest plugin for measuring coverage. | URL |
| 1312 | pytest-marks | 2016_12_03__07_12_20 | Set marks on py.test test methods | URL |
| 1313 | pytest-mock | 2016_09_07__07_04_19 | Thin-wrapper around the mock package for easier use with py.test | URL |
| 1314 | pytest-mpl | 2016_09_07__06_58_27 | Pytest plugin to help with testing figures output from matplotlib | URL |
| 1315 | pytest-timeout | 2016_09_08__23_14_08 | Py.test plugin to abort hanging tests | URL |
| 1316 | pytest-xdist | 2016_09_06__03_21_24 | Py.test xdist plugin for distributed testing and loop-on-failing modes | URL |
| 1317 | pythomics | 2016_11_04__23_44_53 | A multi-omic python package | URL |
| 1318 | python | 2016_09_09__22_33_57 | None | URL |
| 1319 | python-bioext | 2016_09_05__09_34_29 | A few handy bioinformatics tools not already in biopython | URL |
| 1320 | python-chado | 2016_12_09__16_22_21 | Chado library | URL |
| 1321 | python-cluster | 2016_11_08__07_23_12 | Python-cluster is a "simple" package that allows to create several groups (clusters) of objects from a list | URL |
| 1322 | python-consensuscore | 2017_02_18__11_22_33 | 'c++ library of multiple-sequence consensus routines with swig bindings' | URL |
| 1323 | python-dateutil | 2017_02_28__06_42_06 | Extensions to the standard python datetime module | URL |
| 1324 | python-fakemp | 2016_09_10__04_41_09 | Fake multiprocessing pool objects | URL |
| 1325 | python-hppy | 2016_09_05__23_35_49 | An intuitive hyphy interface for python | URL |
| 1326 | python-hyphy-python | 2016_09_05__23_53_55 | Hyphy package interface library | URL |
| 1327 | python-intermine | 2017_04_11__17_59_35 | Intermine webservice client | URL |
| 1328 | python-levenshtein | 2016_09_06__00_40_48 | Python extension for computing string edit distances and similarities. | URL |
| 1329 | python-magic | 2016_09_07__13_12_21 | File type identification using libmagic | URL |
| 1330 | python-omero | 2017_03_30__18_49_55 | None | URL |
| 1331 | python-tripal | 2016_12_09__16_22_44 | Tripal api library | URL |
| 1332 | python-weblogo | 2016_09_07__17_25_43 | Tool for creating sequence logos from biological sequence alignments | URL |
| 1333 | python-wget | 2017_04_11__17_59_35 | Pure python download utility | URL |
| 1334 | pythonpy | 2016_09_05__21_53_23 | The swiss army knife of the command line | URL |
| 1335 | pytriangle | 2016_09_07__09_37_24 | A python interface to the 2d triangulation program triangle | URL |
| 1336 | pyvcf | 2016_09_08__08_02_46 | A variant call format reader for python | URL |
| 1337 | pywdl | 2016_09_25__10_36_44 | A python implementation of a wdl parser and language bindings. | URL |
| 1338 | pyx | 2016_09_05__23_19_40 | Python package for the generation of postscript, pdf, and svg files | URL |
| 1339 | qcli | 2016_09_06__03_35_46 | Qcli | URL |
| 1340 | qiime | 2016_05_10__13_07_59 | Quantitative insights into microbial ecology | URL |
| 1341 | qiime-default-reference | 2016_09_07__19_28_56 | Default reference data files for use with qiime. | URL |
| 1342 | qiimetomaaslin | 2016_11_29__07_10_24 | 'data munging script to change text qiime otu tables to pcl-formatted, maaslin-compatible text files' | URL |
| 1343 | qorts | 2016_10_05__22_08_13 | The qorts software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of rna-seq datasets. | URL |
| 1344 | qsignature | 2017_03_22__12_51_07 | Qsignature is a simple and highly effective method for detecting potential sample mix-ups using distance measurements between snp | URL |
| 1345 | quake | 2017_02_25__18_33_09 | "quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15x), specifically intended for illumina sequencing reads" | URL |
| 1346 | qualimap | 2017_01_27__11_55_15 | Quality control of alignment sequencing data and its derivatives like feature counts | URL |
| 1347 | quast | 2017_02_25__18_31_56 | Quality assessment tool for genome assemblies | URL |
| 1348 | quorum | 2017_02_04__19_02_20 | None | URL |
| 1349 | r | 2016_09_09__21_37_50 | None | URL |
| 1350 | r-abind | 2016_09_05__01_25_39 | combine multidimensional arrays into a single array. this is a generalization of 'cbind' | URL |
| 1351 | r-ada | 2016_12_07__07_19_40 | performs discrete, real, and gentle boost under both exponential and logistic loss | URL |
| 1352 | r-ade4 | 2016_10_25__23_47_55 | multivariate data analysis and graphical display. | URL |
| 1353 | r-agricolae | 2016_11_13__12_03_50 | original idea was presented in the thesis "a statistical analysis tool for agricultural | URL |
| 1354 | r-ahocorasicktrie | 2016_11_04__07_26_55 | aho-corasick is an optimal algorithm for finding many keywords in a text. it can locate | URL |
| 1355 | r-algdesign | 2016_11_13__12_06_22 | algorithmic experimental designs. calculates exact and approximate theory experimental | URL |
| 1356 | r-amap | 2016_09_06__05_37_22 | tools for clustering and principal component analysis (with robust methods, and parallelized | URL |
| 1357 | r-ampvis | 2017_02_07__08_36_58 | None | URL |
| 1358 | r-aod | 2017_01_28__21_58_50 | this package provides a set of functions to analyse overdispersed counts or proportions. | URL |
| 1359 | r-argparse | 2016_09_05__04_25_22 | a command line parser to be used with rscript to write "#!" shebang scripts that gracefully | URL |
| 1360 | r-argparser | 2017_01_21__07_50_18 | cross-platform command-line argument parser written purely in r with | URL |
| 1361 | r-aroma.affymetrix | 2016_11_25__15_57_12 | a cross-platform r framework that facilitates processing of any number of affymetrix | URL |
| 1362 | r-aroma.apd | 2016_11_25__15_51_16 | deprecated. do not start building new projects based on this package. (the (in-house) | URL |
| 1363 | r-aroma.core | 2016_11_25__15_56_20 | core methods and classes used by higher-level aroma.* packages part of the aroma project, | URL |
| 1364 | r-ash | 2016_11_13__19_14_20 | !!python/unicode 'david scott''s ash routines ported from s-plus to r.' | URL |
| 1365 | r-base64 | 2016_09_06__06_11_41 | base 64 encoder/decoder | URL |
| 1366 | r-batch | 2016_09_06__06_39_37 | functions to allow you to easily pass command-line arguments into r, and functions | URL |
| 1367 | r-batchjobs | 2016_09_06__06_31_35 | provides map, reduce and filter variants to generate jobs on batch computing systems | URL |
| 1368 | r-bbmisc | 2016_09_06__06_46_43 | miscellaneous helper functions for and from b. bischl and some other guys at tu dortmund, | URL |
| 1369 | r-bbmle | 2016_12_07__07_21_51 | methods and functions for fitting maximum likelihood models in r. this package modifies | URL |
| 1370 | r-beanplot | 2016_09_06__06_54_04 | plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot. | URL |
| 1371 | r-bh | 2016_09_04__15_40_36 | 'boost provides free peer-reviewed portable c++ source libraries. a large part of | URL |
| 1372 | r-biasedurn | 2017_03_29__16_49_31 | statistical models of biased sampling in the form of univariate and multivariate | URL |
| 1373 | r-bigmemory | 2016_09_08__07_07_45 | create, store, access, and manipulate massive matrices. matrices are allocated to | URL |
| 1374 | r-bigmemory.sri | 2016_09_08__07_10_29 | this package provides a shared resource interface for the bigmemory and synchronicity | URL |
| 1375 | r-bio3d | 2016_09_06__07_11_00 | utilities to process, organize and explore protein structure, sequence and dynamics | URL |
| 1376 | r-biom | 2016_09_08__01_56_42 | this is an r package for interfacing with the biom format. | URL |
| 1377 | r-bit | 2016_10_26__03_40_00 | bitmapped vectors of booleans (no nas), coercion from and to logicals, integers and integer subscripts; fast boolean operators and fast summary statistics. with 'bit' vectors you can store true binary booleans {false,true} at the expense of 1 bit only, on a 32 bit architecture this means factor 32 less ram and ~ factor 32 more speed on boolean operations. due to overhead of r calls, actual speed gain depends on the size of the vector: expect gains for vectors of size > 10000 elements. even for one-time boolean operations it can pay-off to convert to bit, the pay-off is obvious, when such components are used more than once. reading from and writing to bit is approximately as fast as accessing standard logicals - mostly due to r's time for memory allocation. the package allows to work with pre-allocated memory for return values by calling .call() directly: when evaluating the speed of c-access with pre-allocated vector memory, coping from bit to logical requires only 70% of the time for copying from logical to logical; and copying from logical to bit comes at a performance penalty of 150%. the package now contains further classes for representing logical selections: 'bitwhich' for very skewed selections and 'ri' for selecting ranges of values for chunked processing. all three index classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher). | URL |
| 1378 | r-bit64 | 2016_10_26__03_36_56 | package 'bit64' provides serializable s3 atomic 64bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. many fast algorithmic operations such as 'match' and 'order' support interactive data exploration and manipulation and optionally leverage caching. | URL |
| 1379 | r-blockmodeling | 2017_03_30__08_32_12 | the package is primarly ment as an implementation of generalized blockmodeling for | URL |
| 1380 | r-bma | 2016_10_31__07_15_23 | package for bayesian model averaging and variable selection for linear models, generalized | URL |
| 1381 | r-calibrate | 2016_09_06__10_19_36 | 'package for drawing calibrated scales with tick marks on (non-orthogonal) variable | URL |
| 1382 | r-car | 2016_12_09__07_24_10 | ' functions and datasets to accompany j. fox and s. weisberg, an r companion to applied | URL |
| 1383 | r-caroline | 2016_11_21__07_06_46 | 'the caroline r library contains dozens of functions useful for: database migration | URL |
| 1384 | r-catools | 2017_02_15__08_11_22 | !!python/unicode 'contains several basic utility functions including: moving (rolling, | URL |
| 1385 | r-cghflasso | 2016_10_30__07_27_22 | !!python/unicode 'spatial smoothing and hot spot detection using the fused lasso regression' | URL |
| 1386 | r-changepoint | 2017_03_16__16_59_13 | implements various mainstream and specialised changepoint methods for finding single | URL |
| 1387 | r-chbutils | 2016_09_06__11_27_18 | Useful utility functions used at the harvard chan school bioinformatics core | URL |
| 1388 | r-cimpl | 2017_03_22__12_28_34 | None | URL |
| 1389 | r-circlize | 2016_09_08__00_41_33 | circular layout is an efficient way for the visualization of huge amounts of information. | URL |
| 1390 | r-coloc | 2016_09_06__12_40_59 | performs the colocalisation tests described in plagnol et al (2009), wallace et al | URL |
| 1391 | r-combinat | 2016_11_13__12_08_57 | routines for combinatorics | URL |
| 1392 | r-compquadform | 2016_09_05__01_33_38 | computes the distribution function of quadratic forms in normal variables using imhof's | URL |
| 1393 | r-compute.es | 2016_09_07__20_10_01 | this package contains several functions for calculating the most widely used effect | URL |
| 1394 | r-corpcor | 2016_09_06__12_57_45 | efficient estimation of covariance and (partial) correlation | URL |
| 1395 | r-corrplot | 2017_02_17__08_05_22 | the corrplot package is a graphical display of a correlation matrix, confidence interval. | URL |
| 1396 | r-d3heatmap | 2017_03_31__00_04_51 | None | URL |
| 1397 | r-data.table | 2017_01_28__00_32_07 | fast aggregation of large data (e.g. 100gb in ram), fast ordered joins, fast add/modify/delete | URL |
| 1398 | r-dbchip | 2016_09_07__12_44_55 | Chip-seq differential binding | URL |
| 1399 | r-delaporte | 2017_01_11__16_13_05 | provides probability mass, distribution, quantile, random-variate generation, and | URL |
| 1400 | r-deldir | 2017_02_17__22_22_22 | calculates the delaunay triangulation and the dirichlet or voronoi tessellation (with | URL |
| 1401 | r-deoptimr | 2016_09_06__13_51_46 | an implementation of a bespoke jde variant of the differential evolution stochastic | URL |
| 1402 | r-diagram | 2016_09_07__17_04_20 | visualises simple graphs (networks) based on a transition matrix, utilities to plot | URL |
| 1403 | r-digest | 2017_03_30__19_36_44 | implementation of a function 'digest()' for the creation of hash digests of arbitrary | URL |
| 1404 | r-discriminer | 2016_11_07__07_07_31 | functions for discriminant analysis and classification purposes covering various methods | URL |
| 1405 | r-docopt | 2016_09_07__02_55_48 | define a command-line interface by just giving it a description in the specific format. | URL |
| 1406 | r-dorng | 2016_09_06__14_52_52 | this package provides functions to perform reproducible parallel foreach loops, using | URL |
| 1407 | r-dpeak | 2016_09_06__15_19_42 | This package provides functions for fitting dpeak, a statistical framework to deconvolve chip-seq peaks. | URL |
| 1408 | r-dplyr | 2017_01_30__20_41_28 | a fast, consistent tool for working with data frame like objects, both in memory and | URL |
| 1409 | r-drc | 2017_04_05__01_13_46 | None | URL |
| 1410 | r-dunn.test | 2016_09_06__15_26_34 | computes dunn's test (1964) for stochastic dominance and reports the results among | URL |
| 1411 | r-dynamictreecut | 2016_12_21__08_05_11 | contains methods for detection of clusters in hierarchical clustering dendrograms. | URL |
| 1412 | r-ellipse | 2016_09_08__00_47_17 | this package contains various routines for drawing ellipses and ellipse-like confidence | URL |
| 1413 | r-emdbook | 2016_12_07__07_23_59 | auxiliary functions and data sets for "ecological models and data", a book presenting | URL |
| 1414 | r-empiricalfdr.deseq2 | 2016_09_06__16_03_59 | Auxiliary functions for the deseq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate. | URL |
| 1415 | r-exomedepth | 2017_02_01__14_29_49 | calls copy number variants (cnvs) from targeted sequence data, typically exome sequencing | URL |
| 1416 | r-fail | 2016_09_06__16_12_27 | more comfortable interface to work with r data or source files in a key-value fashion. | URL |
| 1417 | r-fastcluster | 2017_02_19__00_06_50 | 'this is a two-in-one package which provides interfaces to both r and python. it implements | URL |
| 1418 | r-fda | 2016_09_07__10_22_10 | 'these functions were developed to support functional data analysis as described in | URL |
| 1419 | r-fdrtool | 2016_09_06__16_29_29 | 'estimates both tail area-based false | URL |
| 1420 | r-fftwtools | 2016_09_06__16_35_20 | 'provides a wrapper for several fftw functions. this package provides access to the | URL |
| 1421 | r-fields | 2017_03_17__13_06_40 | for curve, surface and function fitting with an emphasis on splines, spatial data | URL |
| 1422 | r-findpython | 2016_09_06__16_41_50 | package designed to find an acceptable python binary. | URL |
| 1423 | r-fitdistrplus | 2016_09_06__16_47_46 | extends the fitdistr function (of the mass package) with several functions to help | URL |
| 1424 | r-funr | 2016_09_06__17_33_58 | a small utility which wraps rscript and provides access to all r functions from the | URL |
| 1425 | r-futile.logger | 2016_09_08__23_44_41 | !!python/unicode 'provides a simple yet powerful logging utility. based loosely on | URL |
| 1426 | r-futile.options | 2016_09_07__17_00_20 | !!python/unicode 'a scoped options management framework' | URL |
| 1427 | r-future | 2016_11_25__15_54_37 | !!python/unicode 'a future api for r is provided. in programming, a future is an abstraction | URL |
| 1428 | r-gam | 2016_11_14__07_15_13 | functions for fitting and working with generalized additive models, as described in | URL |
| 1429 | r-gamlss | 2016_11_14__07_12_24 | functions for fitting, displaying and checking gamlss models. | URL |
| 1430 | r-gamlss.data | 2016_11_14__07_07_05 | data for gamlss models. | URL |
| 1431 | r-gamlss.dist | 2016_11_14__07_09_38 | the different distributions used for the response variables in gamlss modelling. | URL |
| 1432 | r-gbm | 2016_11_14__07_18_01 | an implementation of extensions to freund and schapire's adaboost algorithm and friedman's | URL |
| 1433 | r-genabel.data | 2016_12_09__07_32_13 | genabel.data package consists of a data set used by genabel functions | URL |
| 1434 | r-genenet | 2016_09_06__18_01_22 | 'analyzes gene expression (time series) data with focus on the inference of gene networks. | URL |
| 1435 | r-geomap | 2016_09_06__18_46_39 | set of routines for making map projections (forward and inverse), topographic maps, | URL |
| 1436 | r-getopt | 2016_09_07__18_33_45 | package designed to be used with rscript to write ``#!'' shebang scripts that accept | URL |
| 1437 | r-getoptlong | 2016_09_07__23_25_17 | this is yet another command-line argument parser which wraps the powerful perl module | URL |
| 1438 | r-ggally | 2016_12_07__19_08_49 | !!python/unicode 'ggally is designed to be a helper to ggplot2. it contains templates | URL |
| 1439 | r-ggalt | 2016_10_12__01_37_12 | a compendium of 'geoms', 'coords' and 'stats' for 'ggplot2', including splines, 1d | URL |
| 1440 | r-ggdendro | 2016_12_24__07_33_53 | !!python/unicode 'this is a set of tools for dendrograms and tree plots using ''ggplot2''. the | URL |
| 1441 | r-ggplot2 | 2017_03_30__08_33_11 | 'ggproto.r' 'aaa-.r' 'aes-calculated.r' 'aes-colour-fill-alpha.r' 'aes-group-order.r' 'aes-linetype-size-shape.r' 'aes-position.r' 'utilities.r' 'aes.r' 'legend-draw.r' 'geom-.r' 'annotation-custom.r' 'annotation-logticks.r' 'geom-polygon.r' 'geom-map.r' 'annotation-map.r' 'geom-raster.r' 'annotation-raster.r' 'annotation.r' 'autoplot.r' 'axis-secondary.r' 'bench.r' 'bin.r' 'coord-.r' 'coord-cartesian-.r' 'coord-fixed.r' 'coord-flip.r' 'coord-map.r' 'coord-munch.r' 'coord-polar.r' 'coord-quickmap.r' 'coord-transform.r' 'data.r' 'facet-.r' 'facet-grid-.r' 'facet-null.r' 'facet-wrap.r' 'fortify-lm.r' 'fortify-map.r' 'fortify-multcomp.r' 'fortify-spatial.r' 'fortify.r' 'stat-.r' 'geom-abline.r' 'geom-rect.r' 'geom-bar.r' 'geom-bin2d.r' 'geom-blank.r' 'geom-boxplot.r' 'geom-col.r' 'geom-path.r' 'geom-contour.r' 'geom-count.r' 'geom-crossbar.r' 'geom-segment.r' 'geom-curve.r' 'geom-defaults.r' 'geom-ribbon.r' 'geom-density.r' 'geom-density2d.r' 'geom-dotplot.r' 'geom-errorbar.r' 'geom-errorbarh.r' 'geom-freqpoly.r' 'geom-hex.r' 'geom-histogram.r' 'geom-hline.r' 'geom-jitter.r' 'geom-label.r' 'geom-linerange.r' 'geom-point.r' 'geom-pointrange.r' 'geom-quantile.r' 'geom-rug.r' 'geom-smooth.r' 'geom-spoke.r' 'geom-text.r' 'geom-tile.r' 'geom-violin.r' 'geom-vline.r' 'ggplot2.r' 'grob-absolute.r' 'grob-dotstack.r' 'grob-null.r' 'grouping.r' 'guide-colorbar.r' 'guide-legend.r' 'guides-.r' 'guides-axis.r' 'guides-grid.r' 'hexbin.r' 'labeller.r' 'labels.r' 'layer.r' 'layout.r' 'limits.r' 'margins.r' 'plot-build.r' 'plot-construction.r' 'plot-last.r' 'plot.r' 'position-.r' 'position-collide.r' 'position-dodge.r' 'position-identity.r' 'position-jitter.r' 'position-jitterdodge.r' 'position-nudge.r' 'position-stack.r' 'quick-plot.r' 'range.r' 'save.r' 'scale-.r' 'scale-alpha.r' 'scale-brewer.r' 'scale-continuous.r' 'scale-date.r' 'scale-discrete-.r' 'scale-gradient.r' 'scale-grey.r' 'scale-hue.r' 'scale-identity.r' 'scale-linetype.r' 'scale-manual.r' 'scale-shape.r' 'scale-size.r' 'scale-type.r' 'scales-.r' 'stat-bin.r' 'stat-bin2d.r' 'stat-bindot.r' 'stat-binhex.r' 'stat-boxplot.r' 'stat-contour.r' 'stat-count.r' 'stat-density-2d.r' 'stat-density.r' 'stat-ecdf.r' 'stat-ellipse.r' 'stat-function.r' 'stat-identity.r' 'stat-qq.r' 'stat-quantile.r' 'stat-smooth-methods.r' 'stat-smooth.r' 'stat-sum.r' 'stat-summary-2d.r' 'stat-summary-bin.r' 'stat-summary-hex.r' 'stat-summary.r' 'stat-unique.r' 'stat-ydensity.r' 'summary.r' 'theme-elements.r' 'theme.r' 'theme-defaults.r' 'theme-current.r' 'translate-qplot-ggplot.r' 'translate-qplot-lattice.r' 'utilities-break.r' 'utilities-grid.r' 'utilities-help.r' 'utilities-matrix.r' 'utilities-resolution.r' 'utilities-table.r' 'zxx.r' 'zzz.r' | URL |
| 1442 | r-ggrepel | 2017_01_20__18_02_33 | 'provides text and label geoms for ''ggplot2'' that help to avoid overlapping text | URL |
| 1443 | r-giant | 2016_09_06__20_01_59 | toolbox for various enrichment analysis methods and quantification of uncertainty | URL |
| 1444 | r-globaloptions | 2016_09_07__15_46_19 | it provides more controls on the option values such as validation and filtering on | URL |
| 1445 | r-globals | 2016_11_25__15_51_59 | !!python/unicode 'identifies global ("unknown") objects in r expressions by code inspection | URL |
| 1446 | r-gmd | 2016_11_14__07_20_48 | gmd is a package for non-parametric distance measurement between two discrete frequency distributions. | URL |
| 1447 | r-gmodels | 2016_11_13__12_11_31 | various r programming tools for model fitting. | URL |
| 1448 | r-googlevis | 2016_09_07__00_49_13 | 'r interface to google charts api, allowing users to create interactive charts based | URL |
| 1449 | r-gplots | 2017_04_11__17_59_35 | various r programming tools for plotting data, including: - calculating and plotting locally smoothed summary functionals ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to stats::lowess function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements ('balloonplot'), - plotting venn diagrams ('venn'), - displaying open-office style plots ('ooplot'), - plotting multiple data sets on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotci', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space'). | URL |
| 1450 | r-gprofiler | 2017_01_19__07_51_25 | functional enrichment analysis, gene identifier conversion and mapping homologous | URL |
| 1451 | r-grimport | 2017_01_28__17_02_36 | functions for converting, importing, and drawing postscript pictures in r plots. | URL |
| 1452 | r-gsalib | 2016_09_06__21_10_00 | !!python/unicode 'this package contains utility functions used by the genome analysis | URL |
| 1453 | r-gsmoothr | 2016_11_25__15_53_44 | tools rewritten in c for various smoothing tasks | URL |
| 1454 | r-hdrcde | 2016_09_06__21_21_15 | !!python/unicode 'computation of highest density regions in one and two dimensions, | URL |
| 1455 | r-htmltools | 2016_09_06__21_11_45 | tools for html generation and output. | URL |
| 1456 | r-hwriter | 2016_09_07__12_04_05 | Easy-to-use and versatile functions to output r objects in html format | URL |
| 1457 | r-idpmisc | 2017_02_12__03_53_06 | None | URL |
| 1458 | r-idr | 2016_09_07__19_55_15 | 'this is a package for estimating the copula mixture model and plotting correspondence | URL |
| 1459 | r-inline | 2016_09_06__22_11_40 | functionality to dynamically define r functions and s4 methods with inlined c, c++ | URL |
| 1460 | r-inlinedocs | 2016_11_14__17_46_20 | generates rd files from r source code with comments. the main features of the default | URL |
| 1461 | r-ipo | 2016_10_27__06_06_18 | The outcome of xcms data processing strongly depends on the parameter settings. ipo ('isotopologue parameter optimization') is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. ipo uses natural, stable 13c isotopes to calculate a peak picking score. retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. the different parameter settings are achieved by design of experiment. the resulting scores are evaluated using response surface models. | URL |
| 1462 | r-ipo-meta | 2017_01_19__07_49_37 | The outcome of xcms data processing strongly depends on the parameter settings. ipo ('isotopologue parameter optimization') is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. ipo uses natural, stable 13c isotopes to calculate a peak picking score. retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. the different parameter settings are achieved by design of experiment. the resulting scores are evaluated using response surface models. | URL |
| 1463 | r-itertools | 2017_02_19__23_23_55 | None | URL |
| 1464 | r-jsonlite | 2017_01_27__20_10_06 | a fast json parser and generator optimized for statistical data and the web. started | URL |
| 1465 | r-klar | 2016_11_13__12_14_07 | miscellaneous functions for classification and visualization developed at the fakultaet | URL |
| 1466 | r-knitr | 2016_10_26__03_46_41 | Provides a general-purpose tool for dynamic report generation in r using literate programming techniques. | URL |
| 1467 | r-knitrbootstrap | 2016_09_07__04_13_38 | a framework to create bootstrap 3 html reports from knitr rmarkdown. | URL |
| 1468 | r-kriging | 2017_04_05__01_12_56 | None | URL |
| 1469 | r-lambda.r | 2016_09_08__11_15_15 | !!python/unicode 'a language extension to efficiently write functional programs in | URL |
| 1470 | r-leaps | 2016_09_26__21_41_10 | regression subset selection including exhaustive search | URL |
| 1471 | r-learnbayes | 2016_11_13__12_16_33 | learnbayes contains a collection of functions helpful in learning the basic tenets | URL |
| 1472 | r-listenv | 2016_11_25__15_43_51 | !!python/unicode 'list environments are environments that can be indexed similarly | URL |
| 1473 | r-locfit | 2017_03_29__12_45_11 | !!python/unicode 'local regression, likelihood and density estimation.' | URL |
| 1474 | r-logging | 2016_11_14__07_23_21 | logging is a pure r package that implements the ubiquitous log4j package. | URL |
| 1475 | r-longitudinal | 2016_09_07__05_39_12 | 'contains general data structures and | URL |
| 1476 | r-lsd | 2016_09_09__04_56_46 | !!python/unicode 'create lots of colorful plots in a plethora of variations (try the | URL |
| 1477 | r-magrittr | 2016_09_07__00_20_01 | provides a mechanism for chaining commands with a new forward-pipe operator, %>%. | URL |
| 1478 | r-maldiquant | 2016_09_08__04_56_13 | a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight | URL |
| 1479 | r-maldiquantforeign | 2016_09_07__00_27_11 | functions for reading (tab, csv, bruker fid, ciphergen xml, mzxml, mzml, imzml, analyze | URL |
| 1480 | r-matrixeqtl | 2016_12_09__07_34_45 | matrix eqtl is designed for fast eqtl analysis on large datasets. matrix eqtl can | URL |
| 1481 | r-matrixstats | 2017_02_16__16_47_19 | high-performing functions operating on rows and columns of matrices, e.g. col / rowmedians(), | URL |
| 1482 | r-mba | 2016_09_07__00_48_56 | scattered data interpolation with multilevel b-splines | URL |
| 1483 | r-mclust | 2016_09_07__13_29_55 | normal mixture modelling fitted via em algorithm for model-based clustering, classification, | URL |
| 1484 | r-misc3d | 2016_11_13__19_13_38 | !!python/unicode 'a collection of miscellaneous 3d plots, including isosurfaces.' | URL |
| 1485 | r-missforest | 2017_02_20__08_29_36 | None | URL |
| 1486 | r-mitools | 2016_12_09__07_37_13 | tools to perform analyses and combine results from multiple-imputation datasets. | URL |
| 1487 | r-mixomics | 2017_04_11__17_59_35 | 'multivariate methods are well suited to large omics data sets where the number of | URL |
| 1488 | r-mmgenome | 2017_02_07__08_38_05 | None | URL |
| 1489 | r-multicool | 2017_02_17__22_21_35 | !!python/unicode 'a set of tools to permute multisets without loops or hash tables | URL |
| 1490 | r-multitaper | 2016_10_30__07_29_58 | Implements multitaper spectral analysis using discrete prolate spheroidal sequences (slepians) and sine tapers. it includes an adaptive weighted multitaper spectral estimate, a coherence estimate, thomson's harmonic f-test, and complex demodulation. the slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates. | URL |
| 1491 | r-mutationalpatterns | 2016_09_29__23_10_23 | R package for extracting and visualizing mutational patterns in base substitution catalogues | URL |
| 1492 | r-mutoss | 2016_09_07__02_24_19 | the mutoss package and accompanying mutossgui package are designed to ease the application | URL |
| 1493 | r-nanostringnorm | 2016_09_08__01_42_31 | a set of tools for normalizing, diagnostics and visualization of nanostring ncounter | URL |
| 1494 | r-nastiseq | 2017_02_08__07_58_24 | None | URL |
| 1495 | r-nleqslv | 2017_04_05__01_14_31 | None | URL |
| 1496 | r-nor1mix | 2016_09_05__23_36_26 | onedimensional normal mixture models classes, for, e.g., density estimation or clustering | URL |
| 1497 | r-nozzle.r1 | 2016_09_05__23_43_26 | !!python/unicode 'the nozzle package provides an api to generate html reports with | URL |
| 1498 | r-optparse | 2016_11_05__03_08_01 | a command line parser inspired by python's 'optparse' library to be used with rscript | URL |
| 1499 | r-ore | 2016_09_05__23_55_16 | provides an alternative to r's built-in functionality for handling regular expressions, | URL |
| 1500 | r-outliers | 2016_11_14__07_28_36 | a collection of some tests commonly used for identifying outliers. | URL |
| 1501 | r-patpro | 2017_01_09__07_56_47 | quickly and easily visualize longitudinal microbiome profiles using standard output | URL |
| 1502 | r-pcapp | 2016_09_06__00_59_44 | !!python/unicode 'robust pca by projection pursuit' | URL |
| 1503 | r-peer | 2016_12_09__18_15_55 | Peer is a collection of bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. applications of peer have (i) detected batch effects and experimental confounders (ii) increased the number of expression qtl findings by threefold and (iii) allowed inference of intermediate cellular traits, such as transcription factor or pathway activations. this project offers an efficient and versatile c++ implementation of the underlying algorithms with user-friendly interfaces to r and python. | URL |
| 1504 | r-penalized | 2016_11_14__17_50_09 | fitting possibly high dimensional penalized regression models. the penalty structure | URL |
| 1505 | r-permute | 2016_09_08__10_22_23 | a set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. | URL |
| 1506 | r-pheatmap | 2017_01_31__07_45_08 | !!python/unicode 'implementation of heatmaps that offers more control over dimensions | URL |
| 1507 | r-phonr | 2016_09_07__08_45_12 | tools for phoneticians and phonologists, including functions for normalization and | URL |
| 1508 | r-plasmidprofiler | 2017_03_03__15_53_51 | Plasmid profiler | URL |
| 1509 | r-plotly | 2017_04_03__17_52_21 | 'easily translate ggplot2 graphs to an interactive web-based version | URL |
| 1510 | r-plotrix | 2017_04_05__01_12_06 | lots of plots, various labeling, axis and color scaling functions. | URL |
| 1511 | r-pmcmr | 2016_09_07__08_51_13 | the kruskal and wallis one-way analysis of variance by ranks or van der waerden's | URL |
| 1512 | r-png | 2016_09_07__15_56_39 | this package provides an easy and simple way to read, write and display bitmap images | URL |
| 1513 | r-pore | 2016_09_07__21_04_36 | An r package to enable organisation and visualisation of nanopore sequencing data | URL |
| 1514 | r-pracma | 2016_09_06__01_17_35 | ' functions from numerical analysis and linear algebra, numerical optimization, differential | URL |
| 1515 | r-preseqr | 2016_09_06__01_28_13 | estimating the number of species represented r or more times in a random sample. | URL |
| 1516 | r-prettyunits | 2016_12_08__07_17_06 | 'pretty, human readable formatting of quantities. time intervals: 1337000 -> 15d 11h | URL |
| 1517 | r-probmetab | 2016_10_27__06_16_12 | Provides probability ranking to candidate compounds assigned to masses, with the prior assumption of connected sample and additional previous and spectral information modeled by the user. | URL |
| 1518 | r-progress | 2016_12_08__07_19_38 | terminal progress bars. they are configurable, may include percentage, elapsed time, | URL |
| 1519 | r-proj4 | 2016_09_06__01_43_52 | a simple interface to lat/long projection and datum transformation of the proj.4 cartographic | URL |
| 1520 | r-prroc | 2016_12_09__07_39_39 | computes the areas under the precision-recall (pr) and roc curve for weighted (e.g., | URL |
| 1521 | r-pscbs | 2016_09_06__01_59_31 | !!python/unicode 'segmentation of allele-specific dna copy number data and detection | URL |
| 1522 | r-pscl | 2016_11_14__07_31_16 | "bayesian analysis of item-response theory (irt) models, roll call analysis; computing | URL |
| 1523 | r-psych | 2016_09_06__02_05_24 | a general purpose toolbox for personality, psychometrics and experimental psychology. functions | URL |
| 1524 | r-ptw | 2017_02_07__08_35_46 | None | URL |
| 1525 | r-purrr | 2017_01_31__07_47_54 | Make your pure functions purr with the 'purrr' package. this package completes r's functional programming tools with missing features present in other programming languages. | URL |
| 1526 | r-qiimer | 2017_01_31__07_49_45 | open qiime output files in r, compute statistics, and create plots from the data. | URL |
| 1527 | r-qqman | 2016_09_06__02_21_20 | q-q and manhattan plots for gwas data | URL |
| 1528 | r-r.cache | 2016_09_07__15_21_19 | !!python/unicode 'memoization can be used to speed up repetitive and computational | URL |
| 1529 | r-r.devices | 2016_11_25__15_52_52 | functions for creating plots and image files in a unified way regardless of output | URL |
| 1530 | r-r.filesets | 2016_11_25__15_55_25 | 'a file set refers to a set of files located in one or more directories on the file | URL |
| 1531 | r-r.huge | 2016_11_25__15_50_31 | 'deprecated. do not start building new projects based on this package. cross-platform | URL |
| 1532 | r-r.methodss3 | 2016_11_25__15_44_40 | !!python/unicode 'methods that simplify the setup of s3 generic functions and s3 methods. major | URL |
| 1533 | r-r.oo | 2016_11_25__15_45_25 | !!python/unicode 'methods and classes for object-oriented programming in r with or | URL |
| 1534 | r-r.rsp | 2016_11_25__15_49_42 | the rsp markup language makes any text-based document come alive. rsp provides a | URL |
| 1535 | r-r.utils | 2016_11_25__15_48_56 | !!python/unicode 'utility functions useful when programming and developing r packages.' | URL |
| 1536 | r-rainbow | 2017_04_11__17_59_35 | !!python/unicode 'functions and data sets for functional data display and outlier | URL |
| 1537 | r-rann | 2017_03_22__12_50_13 | None | URL |
| 1538 | r-rappdirs | 2016_09_08__06_07_43 | an easy way to determine which directories on the users computer you should use to | URL |
| 1539 | r-rcircos | 2017_02_03__04_13_12 | 'a simple and flexible way to generate circos 2d track plot images for genomic data | URL |
| 1540 | r-rcppgsl | 2016_11_12__11_42_03 | None | URL |
| 1541 | r-rcppparallel | 2017_01_07__07_43_57 | high level functions for parallel programming with 'rcpp'. for example, the 'parallelfor()' | URL |
| 1542 | r-readbrukerflexdata | 2016_09_06__03_27_34 | reads data files acquired by maldi-tof ms on bruker daltonics machines of the *flex | URL |
| 1543 | r-readmzxmldata | 2016_09_06__03_35_28 | functions for reading mass spectrometry data in mzxml format. | URL |
| 1544 | r-readr | 2016_09_30__19_43_37 | read flat/tabular text files from disk (or a connection). | URL |
| 1545 | r-relaimpo | 2016_12_09__07_42_10 | relaimpo provides several metrics for assessing relative importance in linear models. | URL |
| 1546 | r-relations | 2016_10_05__22_43_30 | data structures and algorithms for k-ary relations with arbitrary domains, featuring | URL |
| 1547 | r-reshape2 | 2017_02_04__08_08_18 | 'flexibly restructure and aggregate data using just two functions: melt and ''dcast'' | URL |
| 1548 | r-rfoc | 2016_09_06__04_10_21 | graphics for statistics on a sphere, as applied to geological fault data, crystallography, | URL |
| 1549 | r-rlist | 2016_09_20__13_54_30 | provides a set of functions for data manipulation with list objects, including mapping, | URL |
| 1550 | r-rmarkdown | 2016_09_07__17_57_06 | Convert r markdown documents into a variety of formats. | URL |
| 1551 | r-rniftyreg | 2016_09_08__02_38_36 |
provides an r interface to the niftyreg image registration tools |
URL |
| 1552 | r-robustbase | 2016_10_30__07_32_40 | '"essential" robust statistics. tools allowing to analyze data with robust methods. this | URL |
| 1553 | r-robustrankaggreg | 2016_09_06__05_07_46 | methods for aggregating ranked lists, especially lists of genes. it implements the | URL |
| 1554 | r-rocr | 2016_12_09__07_44_55 | roc graphs, sensitivity/specificity curves, lift charts, and precision/recall plots | URL |
| 1555 | r-rphylip | 2017_02_08__16_31_25 | None | URL |
| 1556 | r-rpmg | 2016_09_08__02_26_01 | really poor man's graphical user interface, used to create interactive r analysis | URL |
| 1557 | r-rrcov | 2016_09_06__05_27_48 | robust location and scatter estimation and robust multivariate analysis with high | URL |
| 1558 | r-rseis | 2016_09_06__05_35_15 | multiple interactive codes to view and analyze seismic data, via spectrum analysis, | URL |
| 1559 | r-rsm | 2016_09_06__05_43_55 | provides functions to generate response-surface designs, fit first- and second-order | URL |
| 1560 | r-rsolnp | 2016_11_25__15_47_59 | general non-linear optimization using augmented lagrange multiplier method. | URL |
| 1561 | r-runit | 2016_09_06__06_03_59 | r functions implementing a standard unit testing framework, with additional code inspection | URL |
| 1562 | r-rwave | 2016_09_06__19_32_46 | 'a set of r functions which provide an environment for the time-frequency analysis | URL |
| 1563 | r-sartools | 2016_09_04__21_35_03 | Sartools provides r tools and an environment for the statistical analysis of rna-seq projects load and clean data, produce figures, perform statistical analysis/testing with deseq2 or edger, export results and create final report. | URL |
| 1564 | r-scales | 2017_01_28__07_59_41 | graphical scales map data to aesthetics, and provide methods for automatically determining | URL |
| 1565 | r-scatterplot3d | 2016_09_06__06_30_06 | plots a three dimensional (3d) point cloud. | URL |
| 1566 | r-scrm | 2016_09_06__06_40_15 | a coalescent simulator that allows the rapid simulation of biological sequences under | URL |
| 1567 | r-sendmailr | 2016_09_06__06_46_21 | package contains a simple smtp client which provides a portable solution for sending | URL |
| 1568 | r-seqinr | 2016_09_06__06_55_18 | exploratory data analysis and data visualization for biological sequence (dna and | URL |
| 1569 | r-sets | 2016_10_07__08_16_31 | data structures and basic operations for ordinary sets, generalizations such as fuzzy | URL |
| 1570 | r-shape | 2016_09_07__15_57_12 | functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, | URL |
| 1571 | r-shinyace | 2017_03_31__00_05_36 | None | URL |
| 1572 | r-signal | 2016_09_07__21_43_37 | a set of signal processing functions originally written for 'matlab' and 'octave'. | URL |
| 1573 | r-skellam | 2017_03_05__02_19_35 | None | URL |
| 1574 | r-sleuth | 2017_02_04__08_11_13 | Sleuth is an r library for analysis of rna-seq experiments for which transcript abundances have been quantified with kallisto. | URL |
| 1575 | r-snow | 2016_09_06__07_49_51 | support for simple parallel computing in r. | URL |
| 1576 | r-snowfall | 2016_09_07__10_02_05 | usability wrapper around snow for easier development of parallel r programs. this | URL |
| 1577 | r-soap-nmr | 2017_02_08__08_01_46 | None | URL |
| 1578 | r-solarius | 2016_09_06__07_58_56 |
solar is the standard software program to perform linkage and association mappings of the quantitative trait loci (qtls) in pedigrees of arbitrary size and complexity. this package allows the user to exploit the variance component methods implemented in solar. it automates such routine operations as formatting pedigree and phenotype data. it also parses the model output and contains summary and plotting functions for exploration of the results. in addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. see |
URL |
| 1579 | r-spam | 2017_03_15__21_39_20 | 'set of functions for sparse matrix algebra. differences with sparsem/matrix are: (1) | URL |
| 1580 | r-sparql | 2016_09_06__08_18_50 | 'use sparql to pose select or update queries to an end-point. ' | URL |
| 1581 | r-spdep | 2016_11_13__12_19_18 | "a collection of functions to create spatial weights matrix objects from polygon contiguities, | URL |
| 1582 | r-speedglm | 2016_11_17__21_19_15 | fitting linear models and generalized linear models to large data sets by updating | URL |
| 1583 | r-splancs | 2016_09_06__08_24_58 | 'the splancs package was written as an enhancement to s-plus for display and analysis | URL |
| 1584 | r-splitstackshape | 2017_02_03__07_46_33 | online data collection tools like google forms often export multiple-response questions | URL |
| 1585 | r-spp | 2017_04_11__17_59_35 | Chip-seq peak caller | URL |
| 1586 | r-statmod | 2017_04_03__14_57_35 | !!python/unicode 'a collection of algorithms and functions to aid statistical modeling. | URL |
| 1587 | r-stringr | 2016_12_09__07_47_19 | a consistent, simple and easy to use set of wrappers around the fantastic 'stringi' | URL |
| 1588 | r-survey | 2016_12_09__07_49_46 | summary statistics, two-sample tests, rank tests, generalised linear models, cumulative | URL |
| 1589 | r-svdialogs | 2016_09_06__09_05_55 | rapidly construct dialog boxes for your gui, including an automatic function assistant | URL |
| 1590 | r-svgui | 2016_09_06__09_16_33 | functions to manage guis from r | URL |
| 1591 | r-testthat | 2017_03_30__19_37_32 | 'auto-test.r' 'colour-text.r' 'compare.r' 'compare-character.r' 'compare-numeric.r' 'compare-time.r' 'context.r' 'describe.r' 'evaluate-promise.r' 'expect-comparison.r' 'expect-equal-to-reference.r' 'expect-equality.r' 'expect-inheritance.r' 'expect-length.r' 'expect-logical.r' 'expect-named.r' 'expect-output.r' 'reporter.r' 'expect-self-test.r' 'expect-that.r' 'expectation.r' 'expectations-matches.r' 'make-expectation.r' 'mock.r' 'old-school.r' 'praise.r' 'reporter-check.r' 'reporter-fail.r' 'reporter-list.r' 'reporter-minimal.r' 'reporter-multi.r' 'reporter-rstudio.r' 'reporter-silent.r' 'reporter-stop.r' 'stack.r' 'reporter-summary.r' 'reporter-tap.r' 'reporter-teamcity.r' 'reporter-zzz.r' 'skip.r' 'source.r' 'test-compiled-code.r' 'test-example.r' 'test-files.r' 'test-package.r' 'test-path.r' 'test-that.r' 'traceback.r' 'try-again.r' 'utils.r' 'watcher.r' | URL |
| 1592 | r-tfmpvalue | 2017_01_28__17_14_30 | in putative transcription factor binding sites (tfbss) identification from sequence/alignments, | URL |
| 1593 | r-tibble | 2017_01_27__00_08_00 | provides a 'tbl_df' class that offers better checking and printing capabilities than | URL |
| 1594 | r-truncnorm | 2016_11_25__15_47_13 | r/d/p/q functions for the truncated normal distribution | URL |
| 1595 | r-tsne | 2017_01_22__07_38_30 | a "pure r" implementation of the t-sne algorithm. | URL |
| 1596 | r-upsetr | 2016_11_07__23_08_28 | creates visualizations of intersecting sets using a novel matrix design, along with | URL |
| 1597 | r-vegan | 2016_11_13__18_11_37 | ordination methods, diversity analysis and other functions for community and vegetation | URL |
| 1598 | r-venndiagram | 2016_09_06__10_33_45 | a set of functions to generate high-resolution venn and euler plots. includes handling | URL |
| 1599 | r-vgam | 2016_12_24__07_36_13 | 'an implementation of about 6 major classes of statistical regression models. at the | URL |
| 1600 | r-viridis | 2016_09_06__10_41_16 | port of the new 'matplotlib' color maps ('viridis' - the default -, 'magma', 'plasma' | URL |
| 1601 | r-wasabi | 2016_09_07__00_08_45 | Prepare sailfish and salmon output for downstream analysis | URL |
| 1602 | r-waveslim | 2017_03_22__12_50_55 | None | URL |
| 1603 | r-wrassp | 2016_10_08__12_37_53 | a wrapper around michel scheffers's libassp (advanced speech signal processor). the | URL |
| 1604 | r-writexls | 2016_09_06__10_54_18 | !!python/unicode 'cross-platform perl based r function to create excel 2003 (xls) | URL |
| 1605 | r-xmlrpc | 2016_09_06__11_11_50 | a simple implementation of xml-rpc for r. | URL |
| 1606 | r-xnomial | 2016_09_30__18_46_14 | Tests whether a set of counts fit a given expected ratio. for example, a genetic cross might be expected to produce four types in the relative frequencies of 9:3:3:1. to see whether a set of observed counts fits this expectation, one can examine all possible outcomes with xmulti() or a random sample of them with xmonte() and find the probability of an observation deviating from the expectation by at least as much as the observed. as a measure of deviation from the expected, one can use the log-likelihood ratio, the multinomial probability, or the classic chi-square statistic. a histogram of the test statistic can also be plotted and compared with the asymptotic curve. | URL |
| 1607 | r-yaml | 2017_01_30__16_10_31 | this package implements the libyaml yaml 1.1 parser and emitter (http://pyyaml.org/wiki/libyaml) | URL |
| 1608 | ra | 2016_09_07__06_20_50 | Ra is short for rna assembler and it is a c++ implementation of an overlap-layout-consensus transcriptome assembler. | URL |
| 1609 | ra-integrate | 2016_09_06__04_17_57 | Integration of the ra assembler - a de novo dna assembler for third generation sequencing data. | URL |
| 1610 | racon | 2017_02_24__08_01_51 | None | URL |
| 1611 | rainbow | 2017_04_11__17_59_35 | Efficient tool for clustering and assembling short reads, especially for rad | URL |
| 1612 | randfold | 2017_01_09__08_06_29 | Minimum free energy of folding randomization test software | URL |
| 1613 | rapclust | 2017_03_04__12_57_51 | Accurate, fast and lightweight clustering of de novo transcriptomes using fragment equivalence classes | URL |
| 1614 | rapsearch | 2016_12_21__08_02_41 | Rapsearch2 is a tool for fast protein similarity searches. | URL |
| 1615 | rascaf | 2017_01_13__07_39_46 | scaffolding with rna-seq read alignment | URL |
| 1616 | raxml | 2016_09_06__07_59_05 | Phylogenetics - randomized axelerated maximum likelihood. | URL |
| 1617 | ray | 2017_04_09__10_05_58 | None | URL |
| 1618 | razers3 | 2016_10_04__14_44_34 | A tool for mapping millions of short genomic reads onto a reference genome | URL |
| 1619 | rdfextras | 2017_01_05__08_06_28 | Rdfextras provide tools, extra stores and such for rdflib. | URL |
| 1620 | rdflib | 2017_02_19__20_03_36 | Rdflib is a pure python package work working with rdf | URL |
| 1621 | rdflib-jsonld | 2017_02_19__20_04_47 | Rdflib extension adding json-ld parser and serializer | URL |
| 1622 | rdkit | 2016_05_15__19_20_52 | "open-source cheminformatics software" | URL |
| 1623 | rdock | 2017_03_11__08_12_35 | None | URL |
| 1624 | rdp-readseq | 2017_01_25__07_41_01 | 'java based common sequence file format reader and sequence file manipulation.' | URL |
| 1625 | rdptools | 2017_01_30__07_48_45 | metaproject for rdp tools | URL |
| 1626 | reago | 2016_11_24__07_07_51 | an assembly tool for 16s ribosomal rna recovery from metagenomic data | URL |
| 1627 | recon | 2016_10_25__07_11_33 | The recon package performs de novo identification and classification of repeat sequence families from genomic sequences. | URL |
| 1628 | recycler | 2017_02_13__13_14_37 | recycler is a tool designed for extracting circular sequences from de novo assembly graphs | URL |
| 1629 | regex | 2016_09_05__23_42_49 | Alternative regular expression module, to replace re. | URL |
| 1630 | relocate2 | 2016_11_18__04_15_35 | None | URL |
| 1631 | remurna | 2016_12_09__07_29_46 | Measurement of single-nucleotide polymorphism-induced changes of rna conformation | URL |
| 1632 | repeatmasker | 2017_04_05__00_17_28 | Repeatmasker is a program that screens dna sequences for interspersed repeats and low complexity dna sequences. | URL |
| 1633 | repeatmodeler | 2017_02_18__16_40_18 | Repeatmodeler is a de-novo repeat family identification and modeling package. | URL |
| 1634 | repeatscout | 2016_10_25__07_27_04 | De novo identification of repeat families in large genomes. | URL |
| 1635 | requests-cache | 2016_09_05__23_46_31 | Persistent cache for requests library | URL |
| 1636 | requests-toolbelt | 2016_09_08__03_39_33 | A toolbelt of useful classes and functions to be used with python-requests | URL |
| 1637 | retry_decorator | 2016_09_05__23_54_54 | Retry decorator | URL |
| 1638 | rgi | 2017_03_17__12_50_13 | This tool provides a preliminary annotation of your dna sequence(s) based upon the data available in the comprehensive antibiotic resistance database (card). hits to genes tagged with antibiotic resistance ontology terms will be highlighted. as card expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. see license at card website | URL |
| 1639 | rgi_conda_dev | 2017_03_17__08_20_44 | None | URL |
| 1640 | ribodiff | 2017_03_10__08_11_56 | None | URL |
| 1641 | riboplot | 2017_03_28__08_21_58 | None | URL |
| 1642 | ribotaper | 2016_08_26__20_32_32 | Ribotaper is a new analysis pipeline for ribosome profiling (ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. | URL |
| 1643 | rmap | 2016_09_29__20_34_53 | Rmap is a short reads mapper for next-generation sequencing data | URL |
| 1644 | rmats | 2016_10_27__06_11_30 | Mats is a computational tool to detect differential alternative splicing events from rna-seq data. | URL |
| 1645 | rmblast | 2017_04_04__12_06_37 | None | URL |
| 1646 | rna-seqc | 2017_03_10__10_27_58 | None | URL |
| 1647 | rnabob | 2016_09_19__07_13_11 | Fast rna motif searching | URL |
| 1648 | rnacode | 2016_05_03__21_43_09 | Rnacode - analyze the protein coding potential in multiple sequence alignments rnacode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. it does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques. | URL |
| 1649 | rnalien | 2017_04_08__13_32_28 | None | URL |
| 1650 | rnashapes | 2016_05_03__21_43_30 | Rnashape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. this avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space. | URL |
| 1651 | rnasnp | 2016_12_14__07_21_02 | Efficient detection of local rna secondary structure changes induced by snps. | URL |
| 1652 | rnastructure | 2016_05_03__21_44_04 | Rnastructure is a complete package for rna and dna secondary structure prediction and analysis. it includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. it also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured rna target. this is useful for sirna design. it can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. finally, rnastructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. these include chemical mapping, enzymatic mapping, nmr, and shape data. | URL |
| 1653 | rnaz | 2016_05_03__21_44_50 | Predicting structural noncoding rnas | URL |
| 1654 | roary | 2017_01_01__07_34_22 | 'rapid large-scale prokaryote pan genome analysis' | URL |
| 1655 | roary2fripan.py | 2016_12_05__07_12_16 | None | URL |
| 1656 | ropebwt2 | 2016_09_06__05_12_27 | Incremental construction of fm-index for dna sequences | URL |
| 1657 | rpy2 | 2016_09_05__08_53_40 | Python interface to the r language (embedded r) | URL |
| 1658 | rsa | 2016_09_05__21_57_11 | Pure-python rsa implementation | URL |
| 1659 | rscape | 2016_11_15__20_02_05 | R-scape (rna structural covariation above phylogenetic expectation) looks for evidence of a conserved rna secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment. | URL |
| 1660 | rseg | 2016_09_06__11_45_53 | The rseg software package is used to analyze chip-seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as h3k36me3 and h3k27me3. | URL |
| 1661 | rsem | 2017_03_16__21_46_40 | rsem (rna-seq by expectation-maximization) | URL |
| 1662 | rseqc | 2017_03_04__08_58_23 | Rna-seq qc package | URL |
| 1663 | ruamel.ordereddict | 2016_09_07__15_41_00 | A version of dict that keeps keys in insertion resp. sorted order | URL |
| 1664 | ruamel.yaml | 2016_09_18__07_04_36 | "a yaml package for python. it is a derivative of kirill simonov's pyyaml 3.11 which supports yaml1.1" | URL |
| 1665 | ruby | 2016_10_03__15_19_57 | None | URL |
| 1666 | ruffus | 2016_09_07__14_49_24 | Light-weight python computational pipeline management | URL |
| 1667 | rust | 2017_01_12__14_31_50 | rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. | URL |
| 1668 | rust-bio-tools | 2016_11_02__20_39_31 | | | URL |
| 1669 | s3gof3r | 2016_09_05__15_47_15 | Fast, concurrent, streaming access to amazon s3, including gof3r, a cli | URL |
| 1670 | sailfish | 2017_03_21__10_20_11 | Rapid mapping-based isoform quantification from rna-seq reads | URL |
| 1671 | sak | 2017_01_28__15_44_13 | This tool allows one to cut sequences and parts of sequences out of sequence files. | URL |
| 1672 | salmon | 2017_03_20__04_32_30 | Highly-accurate & wicked fast transcript-level quantification from rna-seq reads using lightweight alignments | URL |
| 1673 | sam | 2016_05_10__07_23_36 | Sam - sequence alignment and modeling system | URL |
| 1674 | sambamba | 2017_03_12__11_04_04 | Tools for working with sam/bam data | URL |
| 1675 | samblaster | 2016_12_03__05_37_04 | A tool to mark duplicates and extract discordant and split reads from sam files. | URL |
| 1676 | samtools | 2017_03_21__10_19_08 | Tools for dealing with sam, bam and cram files | URL |
| 1677 | savage | 2017_03_16__01_33_12 | savage (strain aware viral genome assembly) reconstructs individual (viral) haplotypes from a mixed sample. | URL |
| 1678 | sbt | 2017_04_11__17_59_35 | None | URL |
| 1679 | scala | 2017_04_11__17_59_35 | None | URL |
| 1680 | scalpel | 2017_03_17__03_21_37 | Sensitive detection of indels (insertions and deletions) | URL |
| 1681 | schavott | 2016_12_24__07_40_32 | 'assembly and scaffolding of bacterial genomes in real time using minion-sequencing.' | URL |
| 1682 | schema | 2016_09_08__09_34_57 | Simple data validation library | URL |
| 1683 | schema-salad | 2017_02_21__12_49_37 | Schema annotations for linked avro data (salad) | URL |
| 1684 | screamingbackpack | 2016_09_08__08_42_02 | Screamingbackpack | URL |
| 1685 | screed | 2016_09_06__00_12_03 | A simple read-only sequence database, designed for short reads | URL |
| 1686 | searchgui | 2017_03_22__22_59_44 | | | URL |
| 1687 | sed | 2016_11_23__02_42_15 | Sed (stream editor) | URL |
| 1688 | seedme | 2016_12_15__07_38_32 | Python rest like client for seedme.org | URL |
| 1689 | segemehl | 2016_09_06__05_31_52 | Short read mapping with gaps | URL |
| 1690 | segmentation-fold | 2017_02_24__08_08_33 | None | URL |
| 1691 | segway | 2016_07_12__10_37_13 | A tool for easy pattern discovery and identification in functional genomics data. | URL |
| 1692 | selectsequencesfrommsa | 2017_03_12__08_03_45 | None | URL |
| 1693 | selscan | 2016_09_06__05_33_56 | A program to calculate ehh-based scans for positive selection in genomes | URL |
| 1694 | semidbm | 2016_10_30__09_59_30 | Cross platform (fast) dbm interface in python | URL |
| 1695 | sentieon | 2016_11_26__11_32_54 | Accelerated performance bioinformatics tools for mapping and variant calling | URL |
| 1696 | seq-gen | 2017_03_26__08_11_19 | None | URL |
| 1697 | seq2c | 2016_09_06__05_35_45 | Cohort based copy number calling in gene regions | URL |
| 1698 | seqbuster | 2016_09_05__15_23_15 | Mirna and isomir annotation | URL |
| 1699 | seqcluster | 2016_11_23__21_56_52 | Small rna analysis from ngs data | URL |
| 1700 | seqkit | 2017_04_01__09_14_47 | Cross-platform and ultrafast toolkit for fasta/q file manipulation | URL |
| 1701 | seqmagick | 2017_04_08__08_28_04 | None | URL |
| 1702 | seqprep | 2016_09_07__10_01_09 | None | URL |
| 1703 | seqtk | 2017_02_27__15_57_42 | Seqtk is a fast and lightweight tool for processing sequences in the fasta or fastq format | URL |
| 1704 | setuptools_cython | 2016_09_05__09_05_32 | Cython setuptools integration | URL |
| 1705 | setuptools_scm | 2016_09_06__00_21_04 | The blessed package to manage your versions by scm tags | URL |
| 1706 | sff2fastq | 2017_01_26__07_39_56 | 'extract 454 genome sequencer reads from a sff file and convert them into a fastq formatted output' | URL |
| 1707 | sga | 2017_04_11__17_59_35 | Sga - string graph assembler. sga is a de novo assembler for dna sequence reads. it is based on gene myers string graph formulation of assembly and uses the fm-index/burrows-wheeler transform to efficiently find overlaps between sequence reads. | URL |
| 1708 | sha2 | 2016_05_08__19_38_20 | Implementation of SHA-256, SHA-384, and SHA-512 hash algorithms | URL |
| 1709 | shape-it | 2017_04_11__17_59_35 | Shape alignment against a database of molecules | URL |
| 1710 | shape_it | 2016_12_14__07_22_48 | None | URL |
| 1711 | sharedmem | 2017_03_08__12_38_25 | None | URL |
| 1712 | shellescape | 2016_09_08__03_29_28 | Shell escape a string to safely use it as a token in a shell command (backport of python shlex.quote for python versions 2.x & < 3.3) | URL |
| 1713 | shorah | 2017_04_02__08_24_31 | None | URL |
| 1714 | sim4db | 2017_01_09__16_47_06 | "sim4db and leaff: utilities for fast batch spliced alignment and sequence indexing" | URL |
| 1715 | simlord | 2017_03_20__15_40_31 | Simlord is a read simulator for long reads from third generation sequencing. currently, it supports the pacific biosciences smrt error model. | URL |
| 1716 | simple_sv_annotation | 2017_02_18__12_08_29 | Simplify snpeff annotations for interesting cases | URL |
| 1717 | simplejson | 2016_09_07__20_24_50 | Simple, fast, extensible json encoder/decoder for python | URL |
| 1718 | sina | 2017_03_02__08_03_08 | None | URL |
| 1719 | sistr_cmd | 2017_02_23__16_36_56 | None | URL |
| 1720 | sixgill | 2016_10_13__13_35_55 | Six-frame genome-inferred libraries for lc-ms/ms | URL |
| 1721 | slang | 2016_09_06__06_20_41 | None | URL |
| 1722 | slclust | 2016_09_06__06_18_18 | A utility that performs single-linkage clustering with the option of applying a jaccard similarity coefficient to break weakly bound clusters into distinct clusters. | URL |
| 1723 | smalt | 2016_09_06__06_23_04 | Smalt aligns dna sequencing reads with a reference genome. | URL |
| 1724 | smartdenovo | 2016_09_06__06_25_34 | Ultra-fast de novo assembler using long noisy reads | URL |
| 1725 | smhasher | 2016_11_18__12_31_56 | Python extension for smhasher hash functions | URL |
| 1726 | snakemake | 2017_03_16__05_56_12 | 'snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. snakemake workflows are essentially python scripts extended by declarative code to define rules. rules describe how to create output files from input files.' | URL |
| 1727 | snap | 2016_09_06__06_29_25 | semi-hmm-based nucleic acid parser -- gene prediction tool | URL |
| 1728 | snap-aligner | 2017_04_11__17_59_35 | Scalable nucleotide alignment program -- a fast and accurate read aligner for high-throughput sequencing data | URL |
| 1729 | sniffles | 2017_03_08__12_48_27 | None | URL |
| 1730 | snippy | 2017_03_22__16_04_47 | Rapid bacterial snp calling and core genome alignments | URL |
| 1731 | snoscan | 2017_02_03__04_10_35 | search for c/d box methylation guide snorna genes in a genomic sequence | URL |
| 1732 | snp-pipeline | 2016_09_05__22_58_07 | Script and functions for snp matrix construction | URL |
| 1733 | snp-sites | 2016_12_15__07_39_01 | 'finds snp sites from a multi-fasta alignment file.' | URL |
| 1734 | snpeff | 2017_04_10__17_56_38 | Genetic variant annotation and effect prediction toolbox | URL |
| 1735 | snpsift | 2016_12_09__13_52_48 | Toolbox that allows you to filter and manipulate annotated files | URL |
| 1736 | soapdenovo-trans | 2017_03_07__08_07_20 | None | URL |
| 1737 | soapdenovo2 | 2016_09_06__06_46_21 | Soapdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. | URL |
| 1738 | soapdenovo2-errorcorrection | 2016_09_07__13_29_35 | Error correction for soapdenovo2. | URL |
| 1739 | soapdenovo2-gapcloser | 2017_04_11__17_59_35 | A tool named gapcloser for soapdenovo. | URL |
| 1740 | soapdenovo2-prepare | 2016_09_05__13_57_19 | Soapdenovo2 data prepare module using assembled contig to do scaffold assembly | URL |
| 1741 | soapec | 2016_09_04__22_13_17 | A correction tool for soapdenovo | URL |
| 1742 | soapsplice | 2017_03_10__08_12_25 | None | URL |
| 1743 | somatic-sniper | 2016_09_05__10_22_56 | A tool to call somatic single nucleotide variants. | URL |
| 1744 | sortedcontainers | 2016_09_08__04_10_31 | Python sorted container types: sortedlist, sorteddict, and sortedset | URL |
| 1745 | sortmerna | 2017_01_15__15_28_57 | Sortmerna is a biological sequence analysis tool for filtering, mapping and otu-picking ngs reads. | URL |
| 1746 | spades | 2017_03_02__02_44_52 | Spades (st. petersburg genome assembler) is intended for both standard isolates and single-cell mda bacteria assemblies. | URL |
| 1747 | spanki | 2017_04_11__17_59_35 | Spanki is a set of tools to facilitate analysis of alternative splicing from rna-seq data. spanki compiles quantitative and qualitative information about junction alignments from input bam files, and analyzes junction-level splicing along with pairwise-defined splicing events. a simulator is also included to evaluate junction detection performance. | URL |
| 1748 | sparqlwrapper | 2016_09_05__23_06_00 | Sparql endpoint interface to python | URL |
| 1749 | sparse-neighbors-search | 2017_02_07__22_07_58 | None | URL |
| 1750 | sparseassembler | 2016_12_19__07_37_08 | a sparse k-mer graph based, memory-efficient genome assembler | URL |
| 1751 | sparsehash | 2016_09_07__22_32_47 | An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! the sparsehash library contains several hash-map implementations, including implementations that optimize for space or speed. these hashtable implementations are similar in api to sgi's hash_map class and the tr1 unordered_map class, but with different performance characteristics. it's easy to replace hash_map or unordered_map by sparse_hash_map or dense_hash_map in c++ code. they also contain code to serialize and unserialize from disk. | URL |
| 1752 | spectacle | 2016_09_07__10_16_40 | This software implements a spectral learning algorithm for hidden markov models for epigenomic data. please see our paper for further details: song, j and chen, k. c. spectacle: fast chromatin state annotation using spectral learning. genome biology, 16:33, 2015. http://genomebiology.com/2015/16/1/33 | URL |
| 1753 | spectra-cluster-cli | 2016_10_13__16_12_40 | this is a stand-alone implementation of the new updated pride cluster algorithm. it is based on the spectra-cluster api and uses a highly similar logic as the hadoop implementation spectra-cluster-hadoop used to build the pride cluster resource. | URL |
| 1754 | spectrassembler | 2017_01_11__11_20_30 | tool (experimental) to compute layout from overlaps with spectral algorithm | URL |
| 1755 | sphinx-argparse | 2017_04_11__17_59_35 | Sphinx extension that automatically document argparse commands and options | URL |
| 1756 | sphinxcontrib-programoutput | 2016_09_05__23_15_23 | Sphinx extension to include program output | URL |
| 1757 | splitmem | 2016_09_06__06_56_04 | Graphical pan-genome analysis with suffix skips | URL |
| 1758 | sprinkles | 2016_09_07__15_11_54 | Plugins! easy! | URL |
| 1759 | sqlalchemy-datatables | 2016_09_07__22_37_37 | Sqlalchemy integration of jquery datatables | URL |
| 1760 | sqlitebrowser | 2016_09_06__22_59_35 | Db browser for sqlite is a high quality, visual, open source tool to create, design, and edit database files compatible with sqlite. | URL |
| 1761 | sqt | 2016_12_07__18_03_39 | Command-line tools for the analysis of high-throughput sequencing data | URL |
| 1762 | sra-tools | 2017_02_28__07_23_44 | the sra toolkit and sdk from ncbi is a collection of tools and | URL |
| 1763 | srprism | 2017_04_11__17_59_35 | Srprism - short read alignment tool | URL |
| 1764 | stacks | 2017_01_07__07_44_55 | Stacks is a software pipeline for building loci from rad-seq | URL |
| 1765 | stacks_summary | 2016_10_10__15_01_16 | Stacks reports generator | URL |
| 1766 | stamp | 2016_09_08__07_06_58 | A graphical software package for analyzing taxonomic and functional profiles. | URL |
| 1767 | star | 2017_03_18__11_05_28 | an rna-seq read aligner. | URL |
| 1768 | star-fusion | 2017_04_11__17_59_35 | A fusion gene caller for star. the fusionfilter tools to create needed index data structures are not included. | URL |
| 1769 | stellar | 2017_01_28__16_37_16 | Stellar is a tool for finding pairwise local alignments between long genomic or very many short sequences. | URL |
| 1770 | strelka | 2017_03_10__08_13_53 | None | URL |
| 1771 | stride | 2017_03_14__14_24_28 | The stride assembler integrates string and de bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions. | URL |
| 1772 | stringtie | 2017_02_25__21_44_20 | Transcriptome assembly and quantification for rna-seq | URL |
| 1773 | strip_it | 2016_09_08__06_47_01 | None | URL |
| 1774 | subread | 2016_09_05__13_46_27 | High-performance read alignment, quantification, and mutation discovery | URL |
| 1775 | suds-jurko | 2016_09_04__22_06_37 | Lightweight soap client (jurko's fork) | URL |
| 1776 | suma_package | 2017_04_11__17_59_35 | Fast and exact comparison of sequences | URL |
| 1777 | sure | 2016_09_06__00_32_53 | Utility belt for automated testing in python for python | URL |
| 1778 | survivor | 2017_04_03__08_24_50 | None | URL |
| 1779 | svgutils | 2017_04_11__17_59_35 | Python svg editor that allows to automatically create publication ready composite svg figures. | URL |
| 1780 | svgwrite | 2016_09_06__00_40_04 | A python library to create svg drawings. | URL |
| 1781 | svtools | 2017_04_04__19_02_32 | Tools for processing and analyzing structural variants | URL |
| 1782 | svtyper | 2017_01_17__12_21_23 | Bayesian genotyper for structural variants | URL |
| 1783 | svviz | 2016_09_06__07_42_07 | A read visualizer for structural variants | URL |
| 1784 | swalign | 2017_04_03__08_26_38 | None | URL |
| 1785 | swarm | 2016_12_24__07_44_10 | A robust and fast clustering method for amplicon-based studies. | URL |
| 1786 | sweepfinder2 | 2016_09_06__07_53_37 | The bwa read mapper. | URL |
| 1787 | swga | 2017_03_02__16_31_55 | Select primer sets for selective whole genome amplification (swga) | URL |
| 1788 | synapseclient | 2016_09_06__07_58_06 | A client for synapse, a collaborative compute space that allows scientists to share and analyze data together. | URL |
| 1789 | t_coffee | 2016_12_20__07_30_01 | A collection of tools for computing, evaluating and manipulating multiple alignments of dna, rna, protein sequences and structures. | URL |
| 1790 | tabulate | 2016_09_07__20_33_20 | Pretty-print tabular data | URL |
| 1791 | tabview | 2017_04_11__17_59_35 | A curses command-line csv and list (tabular data) viewer | URL |
| 1792 | taco | 2017_02_20__07_56_16 | None | URL |
| 1793 | targetfinder | 2016_12_05__07_12_49 | Plant small rna target prediction tool | URL |
| 1794 | task | 2016_03_10__09_20_02 | A command-line to do list manager | URL |
| 1795 | taxonkit | 2017_01_22__11_34_58 | A cross-platform and efficient ncbi taxonomy toolkit | URL |
| 1796 | taxtastic | 2016_09_08__01_49_27 | Tools for taxonomic naming and annotation | URL |
| 1797 | tbb | 2016_09_06__23_13_01 | None | URL |
| 1798 | tbl2asn | 2017_02_22__21_24_30 | Tbl2asn is a program that automates the creation of sequence records for submission to genbank | URL |
| 1799 | tclap | 2016_09_07__13_31_15 | Tclap is a small, flexible library that provides a simple interface for defining and accessing command line arguments. | URL |
| 1800 | tdrmapper | 2017_04_11__17_59_35 | Trna detection and quantification | URL |
| 1801 | tedna | 2017_03_01__08_06_23 | None | URL |
| 1802 | tepid | 2016_11_01__07_17_47 | Tepid uses paired-end illumina sequencing reads to identify novel te variants. | URL |
| 1803 | testfixtures | 2016_09_06__00_57_32 | A collection of helpers and mock objects for unit tests and doc tests. | URL |
| 1804 | tetoolkit | 2017_02_16__07_54_36 | None | URL |
| 1805 | textinput | 2016_09_06__01_01_26 | Streamlined version of stdlib fileinput | URL |
| 1806 | tgt | 2016_10_08__12_50_20 | Textgridtools -- read, write, and manipulate praat textgrid files | URL |
| 1807 | theta2 | 2016_05_08__20_08_51 | Estimate tumor purity and clonal/subclonal copy number aberrations directly from high-throughput dna sequencing data | URL |
| 1808 | tidyp | 2016_09_07__21_18_35 | Program for cleaning up and validating html | URL |
| 1809 | tmux | 2016_03_10__09_20_49 | Tmux is a terminal multiplexer. | URL |
| 1810 | toil | 2017_02_25__11_03_19 | A scalable, efficient, cross-platform and easy-to-use workflow engine in pure python | URL |
| 1811 | toolshed | 2016_09_06__01_05_52 | Flexible and easy file manipulation | URL |
| 1812 | tophat | 2017_01_19__10_24_58 | A spliced read mapper for RNA-Seq | URL |
| 1813 | tophat-recondition | 2016_09_22__07_06_29 | Post-processor for tophat unmapped reads | URL |
| 1814 | toposort | 2016_09_06__01_59_13 | A topological sort algorithm for python. | URL |
| 1815 | tqdm | 2016_09_06__08_34_23 | A fast, extensible progress meter | URL |
| 1816 | trackhub | 2016_09_06__02_02_17 | \ncreate and manage ucsc track hubs from python\n | URL |
| 1817 | transabyss | 2016_09_06__08_41_31 | De novo assembly of rna-seq data using abyss | URL |
| 1818 | transcomb | 2017_02_25__14_40_34 | a sparse k-mer graph based, memory-efficient genome assembler | URL |
| 1819 | transdecoder | 2016_09_04__23_47_01 | transdecoder identifies candidate coding regions within transcript | URL |
| 1820 | treebest | 2017_02_21__20_34_08 | A tool for hierarchically clustering on a sparse graph | URL |
| 1821 | treemix | 2017_02_19__12_21_12 | Treemix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations | URL |
| 1822 | treetime | 2016_10_08__12_55_51 | Maximum-likelihood dating and ancestral inference for phylogenetic trees | URL |
| 1823 | trf | 2017_03_19__21_21_09 | None | URL |
| 1824 | triform2 | 2016_09_06__08_28_37 | Improved sensitivity, specificity and control of false discovery rates in chip-seq peak finding. | URL |
| 1825 | trim-galore | 2017_03_17__16_39_19 | None | URL |
| 1826 | trimadap | 2016_09_06__08_48_49 | Fast but inaccurate adapter trimmer for illumina reads. | URL |
| 1827 | trimal | 2016_11_17__07_13_30 | A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment | URL |
| 1828 | trimmomatic | 2016_07_05__07_00_50 | A flexible read trimming tool for illumina ngs data | URL |
| 1829 | trinculo | 2016_09_06__08_55_20 | A toolkit for carrying out genetic association for multi-category phenotypes. implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping. | URL |
| 1830 | trinity | 2017_03_30__08_34_40 | None | URL |
| 1831 | trinotate | 2017_01_10__07_36_49 | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms | URL |
| 1832 | trnascan-se | 2017_01_31__07_50_35 | trna detection in large-scale genome sequence | URL |
| 1833 | tssar | 2017_03_05__14_59_26 | None | URL |
| 1834 | twobitreader | 2016_09_06__02_09_26 | A fast python package for reading .2bit files (used by the ucsc genome browser) | URL |
| 1835 | typing | 2016_09_06__02_14_41 | Type hints for python | URL |
| 1836 | ucsc-addcols | 2016_09_06__10_24_41 | Sum columns in a text file. | URL |
| 1837 | ucsc-ameme | 2016_09_07__00_27_30 | Find common patterns in dna | URL |
| 1838 | ucsc-autodtd | 2016_09_08__00_15_02 | Give this a xml document to look at and it will come up with a dtd | URL |
| 1839 | ucsc-autosql | 2016_09_06__10_35_33 | Create sql and c code for permanently storing | URL |
| 1840 | ucsc-autoxml | 2016_09_06__10_39_59 | Generate structures code and parser for xml file from dtd-like spec | URL |
| 1841 | ucsc-avecols | 2016_09_06__10_43_40 | Average together columns | URL |
| 1842 | ucsc-axtchain | 2016_09_06__10_47_48 | Chain together axt alignments. | URL |
| 1843 | ucsc-axtsort | 2016_09_06__10_53_46 | Sort axt files | URL |
| 1844 | ucsc-axtswap | 2016_09_06__10_59_35 | Swap source and query in an axt file | URL |
| 1845 | ucsc-axttomaf | 2016_09_06__11_02_10 | Convert from axt to maf format | URL |
| 1846 | ucsc-axttopsl | 2016_09_07__13_11_01 | Convert axt to psl format | URL |
| 1847 | ucsc-bedclip | 2016_09_06__11_09_56 | Remove lines from bed file that refer to off-chromosome places. | URL |
| 1848 | ucsc-bedcommonregions | 2016_09_05__04_46_25 | Create a bed file (just bed3) that contains the regions common to all inputs. | URL |
| 1849 | ucsc-bedcoverage | 2016_09_07__06_58_49 | Analyse coverage by bed files - chromosome by | URL |
| 1850 | ucsc-bedextendranges | 2016_09_06__11_19_36 | Extend length of entries in bed 6+ data to be at least the given length, | URL |
| 1851 | ucsc-bedgeneparts | 2016_09_06__11_22_11 | Given a bed, spit out promoter, first exon, or all introns. | URL |
| 1852 | ucsc-bedgraphpack | 2016_09_07__14_18_30 | Pack together adjacent records representing same value. | URL |
| 1853 | ucsc-bedgraphtobigwig | 2016_09_06__11_26_39 | Convert a bedgraph file to bigwig format. | URL |
| 1854 | ucsc-bedintersect | 2016_09_06__11_29_49 | Intersect two bed files | URL |
| 1855 | ucsc-beditemoverlapcount | 2016_09_06__11_33_19 | Count number of times a base is overlapped by the | URL |
| 1856 | ucsc-bedpileups | 2016_09_06__11_36_11 | Find (exact) overlaps if any in bed input | URL |
| 1857 | ucsc-bedremoveoverlap | 2016_09_06__19_24_57 | Remove overlapping records from a (sorted) bed file. gets rid of | URL |
| 1858 | ucsc-bedrestricttopositions | 2016_09_06__11_48_32 | Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file. | URL |
| 1859 | ucsc-bedsort | 2016_09_06__11_52_52 | Sort a .bed file by chrom,chromstart | URL |
| 1860 | ucsc-bedtobigbed | 2016_09_06__11_57_29 | Convert bed file to bigbed. (bigbed version: 4) | URL |
| 1861 | ucsc-bedtogenepred | 2016_09_08__02_13_22 | Convert bed format files to genepred format | URL |
| 1862 | ucsc-bedtopsl | 2016_09_06__12_04_28 | Convert bed format files to psl format | URL |
| 1863 | ucsc-bedweedoverlapping | 2016_09_06__12_09_47 | Filter out beds that overlap a 'weed.bed' file. | URL |
| 1864 | ucsc-bigbedinfo | 2016_09_06__12_14_21 | Show information about a bigbed file. | URL |
| 1865 | ucsc-bigbednameditems | 2016_09_06__12_17_26 | Extract item of given name from bigbed | URL |
| 1866 | ucsc-bigbedsummary | 2016_05_11__10_15_44 | Extract summary information from a bigbed file. | URL |
| 1867 | ucsc-bigbedtobed | 2016_09_06__12_25_49 | Convert from bigbed to ascii bed format. | URL |
| 1868 | ucsc-bigpsltopsl | 2016_09_06__12_30_27 | Convert bigpsl file to psle | URL |
| 1869 | ucsc-bigwigaverageoverbed | 2016_05_11__11_52_03 | Compute average score of big wig over each bed, which may have introns. | URL |
| 1870 | ucsc-bigwigcat | 2016_09_06__12_36_58 | Merge non-overlapping bigwig files | URL |
| 1871 | ucsc-bigwigcluster | 2016_09_07__20_36_23 | Cluster bigwigs using a hactree | URL |
| 1872 | ucsc-bigwigcorrelate | 2016_09_06__12_40_40 | Correlate bigwig files, optionally only on target regions. | URL |
| 1873 | ucsc-bigwiginfo | 2016_09_08__08_18_15 | Print out information about bigwig file. | URL |
| 1874 | ucsc-bigwigmerge | 2016_09_06__12_45_47 | Merge together multiple bigwigs into a single output bedgraph. | URL |
| 1875 | ucsc-bigwigsummary | 2016_09_06__12_51_01 | Extract summary information from a bigwig file. | URL |
| 1876 | ucsc-bigwigtobedgraph | 2016_09_06__12_55_39 | Convert from bigwig to bedgraph format. | URL |
| 1877 | ucsc-bigwigtowig | 2016_09_06__13_00_18 | Convert bigwig to wig. this will keep more of the same structure of the | URL |
| 1878 | ucsc-blasttopsl | 2016_09_06__13_03_38 | Convert blast alignments to psls. | URL |
| 1879 | ucsc-catdir | 2016_09_06__13_06_39 | Concatenate files in directory to stdout. | URL |
| 1880 | ucsc-catuncomment | 2016_09_07__21_59_58 | Concatenate input removing lines that start with '#' | URL |
| 1881 | ucsc-chainantirepeat | 2016_09_06__13_12_07 | Get rid of chains that are primarily the results of repeats and degenerate dna | URL |
| 1882 | ucsc-chainfilter | 2016_09_06__13_14_43 | Filter chain files. output goes to standard out. | URL |
| 1883 | ucsc-chainmergesort | 2016_09_06__13_17_54 | Combine sorted files into larger sorted file | URL |
| 1884 | ucsc-chainnet | 2016_09_06__13_21_27 | Make alignment nets out of chains | URL |
| 1885 | ucsc-chainprenet | 2016_09_06__13_24_06 | Remove chains that don't have a chance of being netted | URL |
| 1886 | ucsc-chainsort | 2016_09_06__13_26_30 | Sort chains. by default sorts by score. | URL |
| 1887 | ucsc-chainsplit | 2016_09_06__13_32_21 | Split chains up by target or query sequence | URL |
| 1888 | ucsc-chainstitchid | 2016_09_07__23_02_42 | Join chain fragments with the same chain id into a single | URL |
| 1889 | ucsc-chainswap | 2016_09_08__03_28_46 | Swap target and query in chain | URL |
| 1890 | ucsc-chaintoaxt | 2016_09_07__10_22_48 | Convert from chain to axt file | URL |
| 1891 | ucsc-chaintopsl | 2016_09_06__13_45_49 | Convert chain file to psl format | URL |
| 1892 | ucsc-chaintopslbasic | 2016_09_07__05_03_37 | Basic conversion chain file to psl format | URL |
| 1893 | ucsc-checkagpandfa | 2016_09_04__23_35_34 | Takes a .agp file and .fa file and ensures that they are in synch | URL |
| 1894 | ucsc-checkcoveragegaps | 2016_09_06__13_49_31 | Check for biggest gap in coverage for a list of tracks. | URL |
| 1895 | ucsc-checkhgfindspec | 2016_09_06__13_53_33 | Test and describe search specs in hgfindspec tables. | URL |
| 1896 | ucsc-checktablecoords | 2016_09_06__13_58_03 | Check invariants on genomic coords in table(s). | URL |
| 1897 | ucsc-chopfalines | 2016_09_06__14_02_25 | Read in fa file with long lines and rewrite it with shorter lines | URL |
| 1898 | ucsc-chromgraphfrombin | 2016_09_06__14_06_37 | Convert chromgraph binary to ascii format. | URL |
| 1899 | ucsc-coltransform | 2016_09_06__14_15_36 | Add and/or multiply column by constant. | URL |
| 1900 | ucsc-countchars | 2016_09_06__14_19_09 | Count the number of occurrences of a particular char | URL |
| 1901 | ucsc-crtreeindexbed | 2016_09_06__14_23_22 | Create an index for a bed file. | URL |
| 1902 | ucsc-crtreesearchbed | 2016_09_08__09_58_39 | Search a crtree indexed bed file and print all items that overlap query. | URL |
| 1903 | ucsc-dbsnoop | 2016_09_06__14_27_36 | Produce an overview of a database. | URL |
| 1904 | ucsc-dbtrash | 2016_09_08__06_57_35 | Drop tables from a database older than specified n hours | URL |
| 1905 | ucsc-estorient | 2016_09_06__14_35_41 | read ests from a database and determine orientation based on estorientinfo table or direction in gbcdnainfo table. update psls so that the strand reflects the direction of transcription. by default, psls where the direction can't be determined are dropped. | URL |
| 1906 | ucsc-faalign | 2016_09_07__21_33_56 | Align two fasta files | URL |
| 1907 | ucsc-facmp | 2016_09_06__14_47_01 | Compare two .fa files | URL |
| 1908 | ucsc-facount | 2016_09_08__11_09_05 | Count base statistics and cpgs in fa files. | URL |
| 1909 | ucsc-fafilter | 2016_09_05__03_19_46 | Filter fa records, selecting ones that match the specified conditions | URL |
| 1910 | ucsc-fafiltern | 2016_09_06__14_52_24 | Get rid of sequences with too many n's | URL |
| 1911 | ucsc-fafrag | 2016_09_06__14_56_29 | Extract a piece of dna from a .fa file. | URL |
| 1912 | ucsc-fanoise | 2016_09_06__15_01_04 | Add noise to .fa file | URL |
| 1913 | ucsc-faonerecord | 2016_09_06__15_05_29 | Extract a single record from a .fa file | URL |
| 1914 | ucsc-fapolyasizes | 2016_09_06__15_09_43 | Get poly a sizes | URL |
| 1915 | ucsc-farandomize | 2016_09_06__15_14_57 | Program to create random fasta records | URL |
| 1916 | ucsc-farc | 2016_09_08__03_10_52 | Reverse complement a fa file | URL |
| 1917 | ucsc-fasize | 2016_09_06__15_23_48 | Print total base count in fa files. | URL |
| 1918 | ucsc-fasomerecords | 2016_09_06__15_27_20 | Extract multiple fa records | URL |
| 1919 | ucsc-fasplit | 2016_09_06__15_33_19 | Split an fa file into several files. | URL |
| 1920 | ucsc-fastqtofa | 2016_09_06__15_37_36 | Convert from fastq to fasta format. | URL |
| 1921 | ucsc-fatofastq | 2016_09_06__15_46_07 | Convert fa to fastq format, just faking quality values. | URL |
| 1922 | ucsc-fatotab | 2016_09_06__15_51_26 | Convert fa file to tab separated file | URL |
| 1923 | ucsc-fatotwobit | 2016_09_06__15_55_12 | Convert dna from fasta to 2bit format | URL |
| 1924 | ucsc-fatrans | 2016_09_07__00_00_04 | Translate dna .fa file to peptide | URL |
| 1925 | ucsc-featurebits | 2016_09_06__16_03_07 | Correlate tables via bitmap projections. | URL |
| 1926 | ucsc-fetchchromsizes | 2016_09_06__16_06_05 |
used to fetch chrom.sizes information from ucsc for the given |
URL |
| 1927 | ucsc-findmotif | 2016_09_06__16_12_03 | Find specified motif in sequence | URL |
| 1928 | ucsc-gaptolift | 2016_09_06__16_16_40 | Create lift file from gap table(s) | URL |
| 1929 | ucsc-genepredcheck | 2016_09_06__16_21_00 | Validate genepred files or tables | URL |
| 1930 | ucsc-genepredfilter | 2016_09_06__16_24_28 | Filter a genepred file | URL |
| 1931 | ucsc-genepredhisto | 2016_09_06__16_29_01 | Get data for generating histograms from a genepred file. | URL |
| 1932 | ucsc-genepredsinglecover | 2016_09_06__16_32_27 | Create single-coverage genepred files | URL |
| 1933 | ucsc-genepredtobed | 2016_09_05__01_57_43 | Convert from genepred to bed format. does not yet handle genepredext | URL |
| 1934 | ucsc-genepredtofakepsl | 2016_09_06__16_37_11 | Create a psl of fake-mrna aligned to gene-preds from a file or table. | URL |
| 1935 | ucsc-genepredtogtf | 2016_09_06__16_41_24 | Convert genepred table or file to gtf. | URL |
| 1936 | ucsc-genepredtomafframes | 2016_09_08__10_37_04 | Create mafframes tables from a genepreds | URL |
| 1937 | ucsc-getrna | 2017_04_11__17_59_35 | Get mrna for genbank or refseq sequences found in a database | URL |
| 1938 | ucsc-gff3togenepred | 2016_09_07__09_44_24 | Convert a gff3 file to a genepred file | URL |
| 1939 | ucsc-gtftogenepred | 2016_09_08__08_03_02 | Convert a gtf file to a genepred | URL |
| 1940 | ucsc-hggcpercent | 2016_09_07__22_35_32 | Calculate gc percentage in 20kb windows | URL |
| 1941 | ucsc-hgloadbed | 2016_05_11__08_57_36 | Load a generic bed file into database | URL |
| 1942 | ucsc-hgloadchain | 2016_05_11__08_58_54 | Load a generic Chain file into database | URL |
| 1943 | ucsc-hgloadmaf | 2016_05_11__09_00_12 | Load a maf file index into the database | URL |
| 1944 | ucsc-hgloadwiggle | 2016_05_11__09_01_42 | Load a wiggle track definition into database | URL |
| 1945 | ucsc-lavtopsl | 2016_05_11__09_03_43 | Convert blastz lav to psl format | URL |
| 1946 | ucsc-liftover | 2016_05_11__09_05_06 | Move annotations from one assembly to another | URL |
| 1947 | ucsc-liftup | 2016_05_11__09_06_25 | change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf | URL |
| 1948 | ucsc-mafaddirows | 2016_05_11__09_07_50 | add 'i' rows to a maf | URL |
| 1949 | ucsc-mafaddqrows | 2016_05_11__09_09_06 | Add quality data to a maf | URL |
| 1950 | ucsc-mafcoverage | 2016_05_11__09_10_31 | Analyse coverage by maf files - chromosome by | URL |
| 1951 | ucsc-maffetch | 2016_05_11__08_34_46 | get overlapping records from an MAF using an index table | URL |
| 1952 | ucsc-maffilter | 2016_05_11__08_36_05 | Filter out maf files. Output goes to standard out | URL |
| 1953 | ucsc-maffrag | 2016_05_11__08_37_42 | Extract maf sequences for a region from database | URL |
| 1954 | ucsc-maffrags | 2016_05_11__08_38_59 | Collect MAFs from regions specified in a 6 column bed file | URL |
| 1955 | ucsc-mafgene | 2016_05_11__08_40_19 | output protein alignments using maf and genePred | URL |
| 1956 | ucsc-mafmefirst | 2016_05_11__08_41_42 | Move component to top if it is one of the named ones. | URL |
| 1957 | ucsc-maforder | 2016_05_11__08_43_06 | order components within a maf file | URL |
| 1958 | ucsc-mafranges | 2016_05_11__08_44_21 | Extract ranges of target (or query) coverage from maf and | URL |
| 1959 | ucsc-mafsinregion | 2016_05_10__20_39_19 | Extract MAFS in a genomic region | URL |
| 1960 | ucsc-mafspecieslist | 2016_05_10__20_40_41 | Scan maf and output all species used in it. | URL |
| 1961 | ucsc-mafspeciessubset | 2016_05_10__20_42_00 | Extract a maf that just has a subset of species. | URL |
| 1962 | ucsc-mafsplit | 2016_05_10__20_43_21 | Split multiple alignment files | URL |
| 1963 | ucsc-mafsplitpos | 2016_05_10__20_44_40 | Pick positions to split multiple alignment input files | URL |
| 1964 | ucsc-maftoaxt | 2016_05_10__20_46_06 | Convert from maf to axt format | URL |
| 1965 | ucsc-maftopsl | 2016_05_10__20_47_55 | Convert maf to psl format | URL |
| 1966 | ucsc-maftosnpbed | 2016_05_10__20_49_20 | finds SNPs in MAF and builds a bed with their functional consequence | URL |
| 1967 | ucsc-maskoutfa | 2016_09_06__17_00_28 | Produce a masked .fa file given an unmasked .fa and | URL |
| 1968 | ucsc-netchainsubset | 2016_05_10__20_50_52 | Create chain file with subset of chains that appear in the net | URL |
| 1969 | ucsc-netclass | 2016_09_06__17_04_12 | Add classification info to net | URL |
| 1970 | ucsc-netfilter | 2016_09_06__17_07_52 | Filter out parts of net. what passes | URL |
| 1971 | ucsc-netsyntenic | 2016_09_07__19_32_51 | Add synteny info to net. | URL |
| 1972 | ucsc-nettoaxt | 2016_09_06__17_13_37 | Convert net (and chain) to axt. | URL |
| 1973 | ucsc-nettobed | 2016_09_06__17_16_35 | Convert target coverage of net to a bed file. | URL |
| 1974 | ucsc-newpythonprog | 2016_09_08__04_58_37 | Make a skeleton for a new python program | URL |
| 1975 | ucsc-nibfrag | 2016_09_06__17_22_06 | Extract part of a nib file as .fa (all bases/gaps lower case by default) | URL |
| 1976 | ucsc-nibsize | 2016_09_06__17_26_57 | Print size of nibs | URL |
| 1977 | ucsc-oligomatch | 2016_09_05__05_14_32 | Find perfect matches in sequence. | URL |
| 1978 | ucsc-parafetch | 2016_09_06__17_30_07 | Try to fetch url with multiple connections | URL |
| 1979 | ucsc-parasync | 2016_09_06__17_34_18 | Uses parafetch to recursively mirror url to given path | URL |
| 1980 | ucsc-positionaltblcheck | 2016_09_08__03_41_40 | Check that positional tables are sorted | URL |
| 1981 | ucsc-pslcat | 2016_09_07__15_21_32 | Concatenate psl files | URL |
| 1982 | ucsc-pslcdnafilter | 2016_09_06__17_39_30 | filter cdna alignments in psl format. filtering criteria are comparative, selecting near best in genome alignments for each given cdna and non-comparative, based only on the quality of an individual alignment. | URL |
| 1983 | ucsc-pslcheck | 2016_09_06__17_42_13 | Validate psl files | URL |
| 1984 | ucsc-psldropoverlap | 2016_05_10__20_57_58 | Deletes all overlapping self alignments. | URL |
| 1985 | ucsc-pslfilter | 2016_09_06__17_51_38 | Filter out psl file | URL |
| 1986 | ucsc-pslhisto | 2016_09_06__17_54_54 | collect counts on psl alignments for making histograms. these then be analyzed with r, texthistogram, etc. | URL |
| 1987 | ucsc-pslliftsubrangeblat | 2016_09_06__18_00_21 | Lift psls from blat subrange alignments | URL |
| 1988 | ucsc-pslmap | 2016_09_07__01_14_22 | Map psls alignments to new targets using alignments of | URL |
| 1989 | ucsc-pslmrnacover | 2016_09_06__18_09_16 | Make histogram of coverage percentage of mrna in psl. | URL |
| 1990 | ucsc-pslpairs | 2016_09_06__18_11_42 | Join paired ends in psl alignments | URL |
| 1991 | ucsc-pslpartition | 2016_09_06__18_14_19 | Split psl files into non-overlapping sets | URL |
| 1992 | ucsc-pslpostarget | 2016_09_06__18_17_28 | Flip psl strands so target is positive and implicit | URL |
| 1993 | ucsc-pslpretty | 2016_09_06__18_19_50 | Convert psl to human-readable output | URL |
| 1994 | ucsc-pslrecalcmatch | 2016_09_07__04_00_21 | Recalculate match,mismatch,repmatch columns in psl file. | URL |
| 1995 | ucsc-pslreps | 2016_09_06__18_24_35 | Analyze repeats and generate genome-wide best alignments from a | URL |
| 1996 | ucsc-pslscore | 2016_09_06__18_27_30 | Calculate web blat score from psl files | URL |
| 1997 | ucsc-pslselect | 2016_09_06__18_30_04 | Select records from a psl file. | URL |
| 1998 | ucsc-pslsort | 2016_09_06__18_34_52 | Merge and sort pscluster .psl output files | URL |
| 1999 | ucsc-pslstats | 2016_09_07__07_34_42 | Collect statistics from a psl file. | URL |
| 2000 | ucsc-pslswap | 2016_05_11__11_14_03 | swap target and query in psls | URL |
| 2001 | ucsc-psltobed | 2016_09_06__18_45_02 | transform a psl format file to a bed format file. | URL |
| 2002 | ucsc-psltobigpsl | 2016_09_06__18_48_13 | Converts psl to bigpsl input (bed format with extra fields) | URL |
| 2003 | ucsc-psltochain | 2016_09_06__18_54_48 | Convert psl records to chain records | URL |
| 2004 | ucsc-psltopslx | 2016_09_04__14_26_27 | Convert from psl to pslx format, which includes sequences | URL |
| 2005 | ucsc-pslxtofa | 2016_05_11__11_20_50 | Convert pslx (with sequence) to fasta file | URL |
| 2006 | ucsc-qacagplift | 2016_09_08__03_38_18 | Use agp to combine per-scaffold qac into per-chrom qac. | URL |
| 2007 | ucsc-qactoqa | 2016_09_06__19_07_43 | Convert from compressed to uncompressed | URL |
| 2008 | ucsc-qactowig | 2016_09_07__05_43_25 | Convert from compressed quality score format to wiggle format. | URL |
| 2009 | ucsc-qatoqac | 2016_09_06__19_14_23 | Convert from uncompressed to compressed | URL |
| 2010 | ucsc-randomlines | 2016_09_04__15_23_57 | Pick out random lines from file | URL |
| 2011 | ucsc-rasqlquery | 2016_09_08__09_52_28 | Do a sql-like query on a ra file. | URL |
| 2012 | ucsc-ratolines | 2016_09_06__19_20_44 | Output .ra file stanzas as single lines, with pipe-separated fields. | URL |
| 2013 | ucsc-ratotab | 2016_09_08__07_10_32 | Convert ra file to table. | URL |
| 2014 | ucsc-rmfadups | 2016_09_07__03_33_25 | Remove duplicate records in fa file | URL |
| 2015 | ucsc-rowstocols | 2016_09_07__14_09_42 | Convert rows to columns and vice versa in a text file. | URL |
| 2016 | ucsc-spacedtotab | 2016_09_06__20_58_41 | Convert fixed width space separated fields to tab separated | URL |
| 2017 | ucsc-splitfile | 2016_09_06__20_24_48 | Split up a file | URL |
| 2018 | ucsc-splitfilebycolumn | 2016_09_06__19_43_28 | Split text input into files named by column value | URL |
| 2019 | ucsc-sqltoxml | 2016_09_06__23_03_27 | Dump out all or part of a relational database to xml, guided | URL |
| 2020 | ucsc-stringify | 2016_09_07__20_18_07 | Convert file to c strings | URL |
| 2021 | ucsc-subchar | 2016_09_06__20_00_26 | Substitute one character for another throughout a file. | URL |
| 2022 | ucsc-subcolumn | 2016_09_06__20_03_14 | Substitute one column in a tab-separated file. | URL |
| 2023 | ucsc-taillines | 2016_09_06__20_08_00 | Add tail to each line of file | URL |
| 2024 | ucsc-tdbquery | 2016_09_06__20_12_25 | Query the trackdb system using sql syntax. | URL |
| 2025 | ucsc-texthistogram | 2016_09_06__20_15_56 | Make a histogram in ascii | URL |
| 2026 | ucsc-ticktodate | 2016_09_07__05_10_06 | Convert seconds since 1970 to time and date | URL |
| 2027 | ucsc-tolower | 2016_09_07__01_24_25 | Convert upper case to lower case in file. leave other chars alone | URL |
| 2028 | ucsc-toupper | 2016_09_06__20_26_31 | Convert lower case to upper case in file. leave other chars alone | URL |
| 2029 | ucsc-trfbig | 2016_09_07__15_44_30 | Mask tandem repeats on a big sequence file. | URL |
| 2030 | ucsc-twobitdup | 2016_09_06__20_32_41 | Check to see if a twobit file has any identical sequences in it | URL |
| 2031 | ucsc-twobitinfo | 2016_09_06__20_37_28 | Get information about sequences in a .2bit file | URL |
| 2032 | ucsc-twobitmask | 2016_09_07__19_45_01 | Apply masking to a .2bit file, creating a new .2bit file | URL |
| 2033 | ucsc-twobittofa | 2016_09_06__20_43_43 | Convert all or part of .2bit file to fasta | URL |
| 2034 | ucsc-validatefiles | 2016_09_06__20_48_34 | Validates the format of different genomic files. | URL |
| 2035 | ucsc-validatemanifest | 2016_09_06__20_52_30 | Validates the encode3 manifest.txt file. | URL |
| 2036 | ucsc-wigcorrelate | 2016_09_06__20_56_40 | Produce a table that correlates all pairs of wigs. | URL |
| 2037 | ucsc-wigtobigwig | 2016_09_06__20_59_57 | Convert ascii format wig file (in fixedstep, variablestep | URL |
| 2038 | ucsc-wordline | 2016_09_07__07_23_31 | Chop up words by white space and output them with one | URL |
| 2039 | ucsc-xmlcat | 2016_09_07__03_27_10 | Concatenate xml files together, stuffing all records inside a single outer tag. | URL |
| 2040 | ucsc-xmltosql | 2016_09_06__21_13_21 | Convert xml dump into a fairly normalized relational database | URL |
| 2041 | umi_tools | 2017_04_05__17_35_19 | Tools for dealing with unique molecular identifiers | URL |
| 2042 | umis | 2017_02_14__02_06_28 | Tools for processing umi rna-tag data | URL |
| 2043 | unicycler | 2017_01_30__11_48_53 | 'hybrid assembly pipeline for bacterial genomes' | URL |
| 2044 | uritemplate | 2016_09_06__02_19_06 | Python implementation of rfc6570, uri template, and can expand templates up to and including level 4 in that specification. | URL |
| 2045 | urllib3 | 2016_09_06__02_22_47 | Http library with thread-safe connection pooling, file post, and more. | URL |
| 2046 | validators | 2016_09_07__04_49_00 | Python data validation for humans™. | URL |
| 2047 | validictory | 2016_09_06__02_29_02 | General purpose python data validator | URL |
| 2048 | vardict | 2017_02_16__16_58_50 | A sensitive variant caller for both single and paired sample variant calling | URL |
| 2049 | vardict-java | 2017_03_30__21_52_58 | java port of the vardict variant discovery program | URL |
| 2050 | variant-effect-predictor | 2016_10_06__19_49_48 | The vep determines the effect of your variants (snps, insertions, deletions, cnvs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. | URL |
| 2051 | variantbam | 2017_04_11__17_59_35 | Filtering and profiling of next-generational sequencing data using region-specific rules | URL |
| 2052 | varscan | 2016_09_06__09_30_24 | Variant detection in massively parallel sequencing data | URL |
| 2053 | vawk | 2017_01_06__15_48_31 | An awk-like vcf parser | URL |
| 2054 | vcf2db | 2017_03_02__14_02_23 | Create a gemini-compatible database from a vcf | URL |
| 2055 | vcf2maf | 2017_02_14__07_45_01 | Convert a vcf into a maf where each variant is annotated to only one of all possible gene isoforms | URL |
| 2056 | vcfanno | 2017_03_18__01_38_18 | Annotate a vcf with other vcfs/beds/tabixed files | URL |
| 2057 | vcfkit | 2017_01_22__07_47_48 | Assorted utilities for the variant call format | URL |
| 2058 | vcflatten | 2016_09_05__01_49_43 | A command line tool for flattening vcf files down to simpler tsv files. | URL |
| 2059 | vcflib | 2016_09_06__09_46_29 | Command-line tools for manipulating vcf files | URL |
| 2060 | vcftoolbox | 2016_09_06__02_37_15 | Tools for manipulating and parsing vcf files | URL |
| 2061 | vcftools | 2016_09_06__09_56_48 | A set of tools written in perl and c++ for working with vcf files. | URL |
| 2062 | velvet | 2016_09_06__09_59_07 | Sequence assembler for short reads | URL |
| 2063 | verifybamid | 2016_12_04__10_21_49 | verifybamid verifies identity and purity of sequence data | URL |
| 2064 | verse | 2016_09_06__10_05_38 | Verse: a versatile and efficient rna-seq read counting tool | URL |
| 2065 | viennarna | 2017_01_25__15_36_16 | Vienna rna package -- rna secondary structure prediction and comparison | URL |
| 2066 | viral-ngs | 2016_12_15__08_01_23 | A set of scripts and tools for the analysis of viral ngs data | URL |
| 2067 | visceral-evaluatesegmentation | 2017_02_12__07_58_54 | None | URL |
| 2068 | visitor | 2016_09_06__02_40_43 | A tiny pythonic visitor implementation. | URL |
| 2069 | vispr | 2017_02_19__17_38_51 | Vispr is a visualization framework and analysis workflow for crispr/cas9 knockout screens. vispr is designed to display results calculated by mageck. | URL |
| 2070 | vnl | 2017_01_13__11_21_00 | a multi-platform collection of c++ software libraries for computer vision and image understanding. | URL |
| 2071 | voluptuous | 2016_09_07__13_33_51 | Python data validation library | URL |
| 2072 | vphaser2 | 2016_09_06__10_11_42 | V-phaser 2 is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data | URL |
| 2073 | vsearch | 2017_02_18__08_18_34 | "a versatile open source tool for metagenomics (usearch alternative)" | URL |
| 2074 | watchdog | 2016_09_06__10_16_40 | Filesystem events monitoring | URL |
| 2075 | wdltool | 2017_03_27__08_14_21 | None | URL |
| 2076 | web.py | 2016_09_07__19_27_03 | Web.py makes web apps | URL |
| 2077 | weblogo | 2016_08_31__13_25_16 | Web based application designed to generate sequence logos | URL |
| 2078 | wgs-assembler | 2017_02_21__19_56_29 | None | URL |
| 2079 | wham | 2016_09_07__23_30_22 | Structural variant detection and association testing | URL |
| 2080 | wkhtmltopdf | 2016_09_08__11_06_46 | Wkhtmltopdf and wkhtmltoimage are open source (lgplv3) command line tools to render html into pdf and various image formats using the qt webkit rendering engine | URL |
| 2081 | workspace | 2016_09_07__03_10_57 | Workspace overmind | URL |
| 2082 | ws4py | 2016_09_06__03_07_35 | Websocket library for python | URL |
| 2083 | wtforms-alchemy | 2016_09_07__18_56_50 | Generates wtforms forms from sqlalchemy models. | URL |
| 2084 | wtforms-components | 2016_09_06__03_17_49 | Additional fields, validators and widgets for wtforms. | URL |
| 2085 | wub | 2017_04_03__08_34_17 | None | URL |
| 2086 | xgboost | 2016_12_09__07_55_18 | Xgboost python package | URL |
| 2087 | xmlbuilder | 2016_11_15__09_39_55 | Pythonic way to crate xml/(x)html files | URL |
| 2088 | xmltodict | 2017_04_11__17_59_35 | Makes working with xml feel like you are working with json | URL |
| 2089 | xmltramp2 | 2016_11_11__08_42_55 | A modern refactoring of the venerable xmltramp application | URL |
| 2090 | xopen | 2016_12_03__10_40_48 | Open compressed files transparently in python | URL |
| 2091 | xsd | 2016_09_29__07_09_48 | Codesynthesis xsd is an open-source, cross-platform w3c xml schema to c++ data binding compiler. provided with an xml instance specification (xml schema), it generates c++ classes that represent the given vocabulary as well as xml parsing and serialization code. | URL |
| 2092 | xsv | 2017_01_18__22_32_14 | A fast csv toolkit written in rust. | URL |
| 2093 | xtandem | 2016_09_28__13_56_09 | X! tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification | URL |
| 2094 | xtermcolor | 2016_09_25__10_38_39 | Python library for terminal color support (including 256-color support | URL |
| 2095 | yaggo | 2016_09_06__21_28_19 | Yaggo is a tool to generate command line parsers for c++. yaggo stands for "yet another gengetopt" and is inspired by gnu gengetopt. | URL |
| 2096 | yaha | 2016_11_01__07_18_11 | Yaha is an open source, flexible, sensitive and accurate dna aligner designed for single-end reads | URL |
| 2097 | yamllint | 2016_09_06__21_32_05 | A linter for yaml files. | URL |
| 2098 | yanc | 2016_10_30__10_00_58 | Yet another nose colorer | URL |
| 2099 | yara | 2016_09_06__21_34_35 | Yara is an exact tool for aligning dna sequencing reads to reference genomes. | URL |
| 2100 | yasm | 2016_09_06__21_37_01 | Yasm is a complete rewrite of the nasm assembler under the "new" bsd license | URL |
| 2101 | zagros | 2016_11_03__14_04_20 | Zagros is a motif-discovery tool for clip-seq data. | URL |
| 2102 | zeroc-ice | 2017_03_17__13_56_17 | None | URL |
| 2103 | zifa | 2016_09_08__02_00_36 | Dimensionality reduction for zero-inflated single-cell gene expression analysis | URL |
| 2104 | znc | 2016_03_10__09_22_08 | An advanced IRC bouncer | URL |