ABCFGHIJKLMNOPQRSTUVWXY
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INSTRUCTIONS
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We now use curatedTCGAData to download these datasets. See the last column for instructions to download the data using the package in Bioconductor.
See below for Bioconductor package installation. MultiAssayExperiment is included in this installation.
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if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("curatedTCGAData")

library(curatedTCGAData)
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Requirement
https://bioconductor.org/packages/MultiAssayExperiment/
https://bioconductor.org/packages/curatedTCGAData/
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Bug reports
https://github.com/waldronlab/MultiAssayExperiment/issues
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Tiny URLhttp://tinyurl.com/MAEOurls
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Google Link
https://docs.google.com/spreadsheets/d/1Ih64DDS5mqDlYFzDyCY9HAUnxvI1b6hapKP_akFuNPY/edit?usp=sharing
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Scripts
https://github.com/waldronlab/MultiAssayExperiment.TCGA
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https://github.com/waldronlab/MultiAssayExperiment-CCLE
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Cohort NameTCGA CodecuratedTCGAData command in Bioconductor
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Adrenocortical carcinomaACCcuratedTCGAData('ACC', dry.run = FALSE, version = '1.1.38')
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Bladder Urothelial CarcinomaBLCAcuratedTCGAData('BLCA', dry.run = FALSE, version = '1.1.38')
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Breast invasive carcinomaBRCAcuratedTCGAData('BRCA', dry.run = FALSE, version = '1.1.38')
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Cervical squamous cell carcinoma and endocervical adenocarcinoma
CESCcuratedTCGAData('CESC', dry.run = FALSE, version = '1.1.38')
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CholangiocarcinomaCHOLcuratedTCGAData('CHOL', dry.run = FALSE, version = '1.1.38')
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Colorectal adenocarcinomaCOADREAD-
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Colon adenocarcinomaCOADcuratedTCGAData('COAD', dry.run = FALSE, version = '1.1.38')
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Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
DLBCcuratedTCGAData('DLBC', dry.run = FALSE, version = '1.1.38')
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Esophageal carcinomaESCAcuratedTCGAData('ESCA', dry.run = FALSE, version = '1.1.38')
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FFPE Pilot Phase IIFPPP-
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GliomaGBMLGG-
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Glioblastoma multiformeGBMcuratedTCGAData('GBM', dry.run = FALSE, version = '1.1.38')
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Head and Neck squamous cell carcinomaHNSCcuratedTCGAData('HNSC', dry.run = FALSE, version = '1.1.38')
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Kidney ChromophobeKICHcuratedTCGAData('KICH', dry.run = FALSE, version = '1.1.38')
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Pan-kidney cohort (KICH+KIRC+KIRP)KIPAN-
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Kidney renal clear cell carcinomaKIRCcuratedTCGAData('KIRC', dry.run = FALSE, version = '1.1.38')
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Kidney renal papillary cell carcinomaKIRPcuratedTCGAData('KIRP', dry.run = FALSE, version = '1.1.38')
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Acute Myeloid LeukemiaLAMLcuratedTCGAData('LAML', dry.run = FALSE, version = '1.1.38')
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Brain Lower Grade GliomaLGGcuratedTCGAData('LGG', dry.run = FALSE, version = '1.1.38')
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Liver hepatocellular carcinomaLIHCcuratedTCGAData('LIHC', dry.run = FALSE, version = '1.1.38')
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Lung adenocarcinomaLUADcuratedTCGAData('LUAD', dry.run = FALSE, version = '1.1.38')
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Lung squamous cell carcinomaLUSCcuratedTCGAData('LUSC', dry.run = FALSE, version = '1.1.38')
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MesotheliomaMESOcuratedTCGAData('MESO', dry.run = FALSE, version = '1.1.38')
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Ovarian serous cystadenocarcinomaOVcuratedTCGAData('OV', dry.run = FALSE, version = '1.1.38')
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Pancreatic adenocarcinomaPAADcuratedTCGAData('PAAD', dry.run = FALSE, version = '1.1.38')
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Pheochromocytoma and ParagangliomaPCPGcuratedTCGAData('PCPG', dry.run = FALSE, version = '1.1.38')
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Prostate adenocarcinomaPRADcuratedTCGAData('PRAD', dry.run = FALSE, version = '1.1.38')
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Rectum adenocarcinomaREADcuratedTCGAData('READ', dry.run = FALSE, version = '1.1.38')
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SarcomaSARCcuratedTCGAData('SARC', dry.run = FALSE, version = '1.1.38')
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Skin Cutaneous MelanomaSKCMcuratedTCGAData('SKCM', dry.run = FALSE, version = '1.1.38')
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Stomach adenocarcinomaSTADcuratedTCGAData('STAD', dry.run = FALSE, version = '1.1.38')
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Stomach and Esophageal carcinomaSTES-
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Testicular Germ Cell TumorsTGCTcuratedTCGAData('TGCT', dry.run = FALSE, version = '1.1.38')
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Thyroid carcinomaTHCAcuratedTCGAData('THCA', dry.run = FALSE, version = '1.1.38')
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ThymomaTHYMcuratedTCGAData('THYM', dry.run = FALSE, version = '1.1.38')
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Uterine Corpus Endometrial CarcinomaUCECcuratedTCGAData('UCEC', dry.run = FALSE, version = '1.1.38')
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Uterine CarcinosarcomaUCScuratedTCGAData('UCS', dry.run = FALSE, version = '1.1.38')
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Uveal MelanomaUVMcuratedTCGAData('UVM', dry.run = FALSE, version = '1.1.38')
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