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 for more information about solar. 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