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• Differences between FPKM and FPKM-UQ files in gene expression analysis
  Hi guys, I am planning to perform a pan-cancer gene expression analysis across several cancer typ...
• TCGA COAD and READ annotations missing from GDC commons?
  I used to download data from the old TCGA annotations manager to identify DNU cases, but I could ...
• What preprocessing steps are required for the different TCGA/GDC Gene Expression Data (Counts, FPKM-UQ)?
  Hi there, I want to use the gene expression data from GDC/TCGA for further analysis, e.g. cluster...
• How to download triple negative breast cancer RNA-seq fpkm data from GDC.
  Hello, This might be a silly question but I couldn't find a tag to select triple negative breast ...
• TCGA data, relationship between different sources
  I am to analyze TCGA data for RNA-Seq of many tumors. I found that data can be downloaded either...
• How to download *.FPKM-UQ.txt.gz files from TCGA GDC for some certain samples using python?
  Hi to all, Is there a way to download transcriptome expression files for some certain sample ids...
• mismatch sample number TCGA ovary cancer between recount and GDC portal
  Hello there! I have been trying to understand what's going on with the RNA-seq TCGA ovary datase...
• TCGA/GDC FPKM vs FPKM-UQ
  GDC provides RNA-seq quantification in multiple forms: > For mRNA-Seq data, the GDC generates...
• From TCGA to GDC (Genomic data commons)
  Hello, I was using TCGA data related to Colon adenocarcinoma (COAD). In the specific I was using...
• raw count on TCGA/GDC
  How do get the RAW COUNT from TCGA/GDC for analysis in R? I only want processed data.
• Alternatives to TCGAbiolinks todownload the TCGA Data
  Hi All, **library(TCGAbiolinks)** is giving errors as *gridExtra* was renamed so I can not use i...
• Querying raw TCGA sequencing data on GDC
  I realized that TCGA Data Access moved from cghub to GDC. Before the move i was using cquery and ...
• GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
  TCGA has recently migrated to the Genomic Data Commons (GDC). Following this migration, many tool...
• the question about new TCGA Rnaseq data
  I find people often use rsem normalized result of TCGA Rnaseq data in DCC server, but i can't fi...
• Download TCGA cancer and normal tissue gene expression data from GDC
  Hi, SInce TCGA data are now on NCI website how can I download gene expression data (FPKM) for br...
• TCGA gene models and exon/isoform level expression data
  Hello I have downloaded mRNA expression data from TCGA-BLCA using TCGAbiolinks. I noticed that t...
• Using GenomeDataCommons and associating UUIDs with RNA-seq files
  I'm using the GDC package to obtain gene expression data. Right now, I'm attempting to associate ...