Broad GDAC stddata__2016_01_28 Run Status : COAD

Cohort	BCR	Clinical	CN	LowP	Methylation	mRNA	mRNASeq	miR	miRSeq	RPPA	MAF	rawMAF
COAD	460	458	451	69	457	153	457	0	406	360	154	367

Note that the links below require Broad internal Firehose login credentials.

	Pipeline Dataset	Not Available	Successful
1	Clinical_Pick_Tier1	0	1
2	CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB	1	0
3	CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT	1	0
4	CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB	1	0
5	CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT	1	0
6	CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB	1	0
7	CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT	1	0
8	CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB	1	0
9	CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT	1	0
10	CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB	1	0
11	CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT	1	0
12	Merge_Clinical	0	1
13	Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg	1	0
14	Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg	1	0
15	Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg	1	0
16	Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg	1	0
17	Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg	0	1
18	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data	1	0
19	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data	1	0
20	Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data	1	0
21	Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data	0	1
22	Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data	0	1
23	Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data	1	0
24	Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data	1	0
25	Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data	0	1
26	Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data	0	1
27	Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data	0	1
28	Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data	0	1
29	Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data	0	1
30	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data	1	0
31	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data	1	0
32	Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data	1	0
33	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data	0	1
34	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data	0	1
35	Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data	0	1
36	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data	1	0
37	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data	1	0
38	Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data	1	0
39	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data	1	0
40	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data	1	0
41	Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data	1	0
42	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data	0	1
43	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data	0	1
44	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data	0	1
45	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data	0	1
46	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__data	0	1
47	Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data	0	1
48	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data	0	1
49	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data	0	1
50	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data	0	1
51	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data	0	1
52	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__data	0	1
53	Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data	0	1
54	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed	0	1
55	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg	0	1
56	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg	0	1
57	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg	0	1
58	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg	0	1
59	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg	1	0
60	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg	1	0
61	Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg	1	0
62	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg	1	0
63	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg	1	0
64	Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg	1	0
65	Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	1	0
66	Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	1	0
67	Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	1	0
68	Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	1	0
69	Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data	0	1
70	Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data	0	1
71	Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data	1	0
72	Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data	1	0
73	Methylation_Preprocess	0	1
74	miRseq_Mature_Preprocess	0	1
75	miRseq_Preprocess	0	1
76	mRNA_Preprocess_Median	0	1
77	mRNAseq_Preprocess	0	1
78	Mutation_Oncotator_Calls	821	154
79	Mutation_Oncotator_Raw_Calls	608	367
80	Mutation_Packager_Calls	0	1
81	Mutation_Packager_Coverage	0	1
82	Mutation_Packager_Oncotated_Calls	0	1
83	Mutation_Packager_Oncotated_Raw_Calls	0	1
84	Mutation_Packager_Raw_Calls	0	1
85	Mutation_Packager_Raw_Coverage	0	1
86	RPPA_AnnotateWithGene	0	1
	Total	1469	565

This table generated on Wed Mar 2 19:32:25 2016

Broad GDAC Standard Data Status stddata__2016_01_28 Run for Tumor Type: COAD

Broad GDAC Standard Data Status
stddata__2016_01_28 Run for Tumor Type: COAD