{"cohort":"TCGA Pan-Cancer (PANCAN)","probeMap":"probeMap/gencode.v23.annotation.transcript.probemap","dataSubType":"transcript expression RNAseq","label":"TOIL RSEM fpkm","name":"tcga_RSEM_isoform_fpkm","dataproducer":"UCSC TOIL RNA-seq recompute","wrangling_procedure":"Data (file names: *.rsem_isoforms.results) are downloaded, fpkm values are extracted, log2(x+0.001) transformed, and combined.","type":"genomicMatrix","version":"2016-09-01","unit":"log2(fpkm+0.001)"}

{"cohort":"TCGA Pan-Cancer (PANCAN)","probeMap":"probeMap/gencode.v23.annotation.transcript.probemap","dataSubType":"transcript expression RNAseq","label":"TOIL RSEM tpm","name":"tcga_rsem_isoform_tpm","dataproducer":"UCSC TOIL RNA-seq recompute","wrangling_procedure":"Data (file names: *.rsem_isoforms.results) are downloaded, tpm values are extracted, log2(x+0.001) transformed, and combined.","type":"genomicMatrix","version":"2016-09-01","unit":"log2(tpm+0.001)","platform":"ILLUMINA"}

{"cohort":"TCGA Pan-Cancer (PANCAN)","probeMap":"probeMap/gencode.v23.annotation.transcript.probemap","dataSubType":"transcript expression RNAseq","label":"TOIL RSEM isoform percentage","name":"tcga_rsem_isopct","dataproducer":"UCSC TOIL RNA-seq recompute","wrangling_procedure":"Data (file names: *.rsem_isoforms.results) are downloaded, IsoPct values are extracted and combined.","type":"genomicMatrix","version":"2016-09-01","unit":"IsoPct"}

{"name":"mc3.v0.2.8.PUBLIC.toil.xena","cohort":"TCGA TARGET GTEx","type":"mutationVector","assembly":"hg19","label":"TCGA somatic mutations (Pan-cancer Atlas MC3 public version)","dataSubType":"somatic mutation (SNP and INDEL)","url":"https://www.synapse.org/#!Synapse:syn7214402/wiki/405297, https://www.synapse.org/#!Synapse:syn7824274","version":"2018-05-08","wrangling_procedure":"downlaod mc3.v0.2.8.PUBLIC.maf.gz, only kept mutations with filter=PASS, only kept samples from the TOIL RNAseq recompute"}

{"name":"TCGA_GTEX_category.txt","type":"clinicalMatrix","version":"2017-06-23","cohort":"TCGA TARGET GTEx","dataSubType":"phenotype","label":"TCGA GTEX main categories","clinicalfeature":"TcgaTargetGTEX_phenotype_clinFeature","wrangling_procedure":"For GTEx, _study = GTEX and _sample_type = \"Normal Tissue\"  _primary_site =  for each category of the gtex list; For TCGA, _study=TCGA, _sample_type != \"Control Analyte\" and != \"Solid Tissue Normal\", detailed_category = each category for the tcga list"}