Broad GDAC Analyses Status
dev Run for Tumor Type: HNSC
Cohort
BCR
Clinical
CN
LowP
Methylation
mRNA
mRNASeq
miR
miRSeq
RPPA
MAF
HNSC
528
494
522
108
528
0
497
0
523
212
306
Note that the links below require Broad internal Firehose login credentials.
Pipeline
NotRunnable
Runnable
InProcess
Successful
Unsuccessful
1
Clinical_Pick_Tier1
0
0
0
1
0
2
CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB
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3
CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT
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0
0
0
0
4
CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB
1
0
0
0
0
5
CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT
1
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6
CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB
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0
0
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7
CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT
1
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8
CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB
1
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9
CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT
1
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10
CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB
1
0
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11
CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT
1
0
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0
0
12
Merge_Clinical
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1
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13
Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_2__bioassay_data_transformation__data
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14
Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg
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15
Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_2__lowess_global_normalization__data
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Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg
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17
Merge_cna__hg_cgh_244a__mskcc_org__Level_2__bioassay_data_transformation__data
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18
Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
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19
Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_2__lowess_global_normalization__data
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20
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0
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0
21
Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
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0
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1
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22
Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data
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23
Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
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24
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25
Merge_methylation__humanmethylation27__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
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0
0
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0
26
Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
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27
Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
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0
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1
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28
Merge_methylation__illuminadnamethylation_oma003_cpi__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
0
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29
Merge_mirna__h_mirna_8x15k__unc_edu__Level_2__unc_quantile_normalization__data
1
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30
Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
1
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31
Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_2__unc_quantile_normalization__data
1
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32
Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
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33
Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
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1
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34
Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
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1
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35
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1
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36
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1
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37
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1
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38
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0
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0
0
39
Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data
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40
Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
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41
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
1
0
0
0
0
42
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data
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43
Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data
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44
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data
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0
0
0
0
45
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data
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0
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0
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46
Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
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0
47
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0
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1
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48
Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
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1
0
49
Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data
0
0
0
1
0
50
Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data
1
0
0
0
0
51
Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data
1
0
0
0
0
52
Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
1
0
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0
53
Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
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54
Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data
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55
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1
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56
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data
0
0
0
1
0
57
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
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1
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58
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
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0
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1
0
59
Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data
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1
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60
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__after_5NN_copy_number__data
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0
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0
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61
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed
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1
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62
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copynumber_byallele__data
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63
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copy_number__data
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64
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data
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0
0
0
66
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg
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1
0
67
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
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0
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1
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68
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
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1
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69
Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg
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0
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1
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70
Merge_snp__human1mduo__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
71
Merge_snp__human1mduo__hudsonalpha_org__Level_2__B_allele_freq__data
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0
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0
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Merge_snp__human1mduo__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
1
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0
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Merge_snp__human1mduo__hudsonalpha_org__Level_2__genotyping__data
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Merge_snp__human1mduo__hudsonalpha_org__Level_2__Normal_LogR__data
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Merge_snp__human1mduo__hudsonalpha_org__Level_2__Paired_LogR__data
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Merge_snp__human1mduo__hudsonalpha_org__Level_2__Unpaired_LogR__data
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77
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg
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0
0
0
0
78
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg
1
0
0
0
0
79
Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
80
Merge_snp__humanhap550__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
81
Merge_snp__humanhap550__hudsonalpha_org__Level_2__B_allele_freq__data
1
0
0
0
0
82
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
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0
0
0
0
83
Merge_snp__humanhap550__hudsonalpha_org__Level_2__genotyping__data
1
0
0
0
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84
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Normal_LogR__data
1
0
0
0
0
85
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Paired_LogR__data
1
0
0
0
0
86
Merge_snp__humanhap550__hudsonalpha_org__Level_2__Unpaired_LogR__data
1
0
0
0
0
87
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg
1
0
0
0
0
88
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg
1
0
0
0
0
89
Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
90
Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
91
Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
92
Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
93
Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
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0
0
0
0
94
Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
95
Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
96
Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data
1
0
0
0
0
97
Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data
1
0
0
0
0
98
mRNAseq_Preprocess
0
0
0
1
0
99
Mutation_Packager_Calls
0
1
0
0
0
100
Mutation_Packager_Coverage
0
1
0
0
0
101
RPPA_AnnotateWithGene
0
0
0
1
0
102
TP-Clinical_Pick_Tier1
0
0
0
1
0
103
TP-CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB
1
0
0
0
0
104
TP-CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT
1
0
0
0
0
105
TP-CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB
1
0
0
0
0
106
TP-CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT
1
0
0
0
0
107
TP-CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB
1
0
0
0
0
108
TP-CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT
1
0
0
0
0
109
TP-CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB
1
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0
0
110
TP-CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT
1
0
0
0
0
111
TP-CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB
1
0
0
0
0
112
TP-CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT
1
0
0
0
0
113
TP-Merge_Clinical
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1
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114
TP-Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_2__bioassay_data_transformation__data
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115
TP-Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg
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116
TP-Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_2__lowess_global_normalization__data
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117
TP-Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg
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118
TP-Merge_cna__hg_cgh_244a__mskcc_org__Level_2__bioassay_data_transformation__data
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119
TP-Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
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120
TP-Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_2__lowess_global_normalization__data
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121
TP-Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg
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122
TP-Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
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123
TP-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data
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124
TP-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
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125
TP-Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data
1
0
0
0
0
126
TP-Merge_methylation__humanmethylation27__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
1
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0
0
0
127
TP-Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
1
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0
0
0
128
TP-Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
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1
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129
TP-Merge_methylation__illuminadnamethylation_oma003_cpi__jhu_usc_edu__Level_2__within_bioassay_data_set_function__data
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TP-Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data
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TP-Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
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135
TP-Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
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136
TP-Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
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137
TP-Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
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138
TP-Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
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139
TP-Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data
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TP-Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data
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TP-Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
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TP-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data
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146
TP-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data
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147
TP-Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
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148
TP-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
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149
TP-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
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150
TP-Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data
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151
TP-Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data
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152
TP-Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data
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153
TP-Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
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154
TP-Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
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155
TP-Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data
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0
465
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed
0
0
0
1
0
466
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copynumber_byallele__data
1
0
0
0
0
467
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__copy_number__data
1
0
0
0
0
468
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data
1
0
0
0
0
469
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__no_outlier_copy_number__data
1
0
0
0
0
470
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg
0
0
0
1
0
471
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
0
0
0
1
0
472
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
0
0
0
1
0
473
NB-Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg
0
0
0
1
0
474
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
475
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__B_allele_freq__data
1
0
0
0
0
476
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
1
0
0
0
0
477
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__genotyping__data
1
0
0
0
0
478
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__Normal_LogR__data
1
0
0
0
0
479
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__Paired_LogR__data
1
0
0
0
0
480
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_2__Unpaired_LogR__data
1
0
0
0
0
481
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg
1
0
0
0
0
482
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg
1
0
0
0
0
483
NB-Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
484
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_1__XandYintensity__data
1
0
0
0
0
485
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__B_allele_freq__data
1
0
0
0
0
486
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__Delta_B_allele_freq__data
1
0
0
0
0
487
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__genotyping__data
1
0
0
0
0
488
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__Normal_LogR__data
1
0
0
0
0
489
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__Paired_LogR__data
1
0
0
0
0
490
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_2__Unpaired_LogR__data
1
0
0
0
0
491
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg
1
0
0
0
0
492
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg
1
0
0
0
0
493
NB-Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg
1
0
0
0
0
494
NB-Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
495
NB-Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
496
NB-Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
497
NB-Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
498
NB-Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data
1
0
0
0
0
499
NB-Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
1
0
0
0
0
500
NB-Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data
1
0
0
0
0
501
NB-Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data
1
0
0
0
0
502
NB-mRNAseq_Preprocess
1
0
0
0
0
503
NB-Mutation_Packager_Calls
1
0
0
0
0
504
NB-Mutation_Packager_Coverage
1
0
0
0
0
505
NB-RPPA_AnnotateWithGene
1
0
0
0
0
Total
407
6
0
92
0
This table generated on Wed Feb 18 16:33:59 2015