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]
methylationcnmf	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.Methylation_Clustering_CNMF.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
mRNAseqhc	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
miRseqcnmf	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.miRseq_Clustering_CNMF.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
miRseqMaturehc	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.miRseq_Mature_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
copynumber	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.CopyNumber_Clustering_CNMF.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
miRseqhc	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.miRseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
mRNAseqcnmf	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.mRNAseq_Clustering_CNMF.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
miRseqMaturecnmf	TGCT-TP.bestclus.txt	gdac.broadinstitute.org_TGCT-TP.miRseq_Mature_Clustering_CNMF.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2014101700	TGCT-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_TGCT-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014101700.0.0	yes
