Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
miRseqcnmf	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.miRseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mRNAseqcnmf	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqMaturehc	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.miRseq_Mature_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
PredictionU133aPhilips	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.RPPA_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mRNAseqhc	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqMaturecnmf	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.miRseq_Mature_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mrnahc	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.mRNA_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
copynumber	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mrnacnmf	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.mRNA_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
PredictionU133aTCGA	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.RPPA_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqhc	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.miRseq_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
methylationcnmf	BRCA-TP.bestclus.txt	gdac.broadinstitute.org_BRCA-TP.Methylation_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	BRCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
