TCGA uterine carcinosarcoma (UCS) PARADIGM inference activity (RNAseq + CNV)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA uterine carcinosarcoma (UCS) somatic mutation (broad curated)","cohort":"TCGA Uterine Carcinosarcoma (UCS)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ucs/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/UCS/mutation_curated_broad","anatomical_origin":["Uterus"],"name":"TCGA.UCS.sampleMap/mutation_curated_broad","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-09-08","version":"2017-09-08","gdata_tags":["Broad Institute Genome Sequencing Center"],"primary_disease":"uterine carcinosarcoma","platform":"IlluminaGA","description":"TCGA uterine carcinosarcoma (UCS) somatic mutation data. Sequencing data are generated on a IlluminaGA system. The calls are generated at Broad Institute Genome Sequencing Center using the MuTect method.","wholegenome":true}

TCGA uterine carcinosarcoma (UCS) somatic mutation (broad curated)

{"name":"GDC-PANCAN/Xena_Matrices/GDC-PANCAN.GDC_phenotype.tsv","cohort":"GDC Pan-Cancer (PANCAN)","url":"https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90, https://api.gdc.cancer.gov/data/","dataSubType":"phenotype","dataproducer":"Genomic Data Commons","label":"Phenotype","type":"clinicalMatrix","wrangler":"Xena GDC ETL script","version":"12-14-2017"}

{"cohort":"GDC Pan-Cancer (PANCAN)","url":"https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90, https://api.gdc.cancer.gov/data/","probeMap":"probeMaps/gencode.v22.annotation.gene.probeMap","dataSubType":"gene expression RNAseq","label":"HTSeq - Counts","name":"GDC-PANCAN/Xena_Matrices/GDC-PANCAN.htseq_counts.tsv","dataproducer":"Genomic Data Commons","wrangling_procedure":"Data from the same sample but from different vials/portions/analytes/aliquotes is averaged; data from different samples is combined into genomicMatrix; all data is then log2(x+1) transformed.","type":"genomicMatrix","wrangler":"Xena GDC ETL script","version":"12-11-2017","unit":"log2(count+1)","platform":"Illumina","colnormalization":true}