This is a test version of Biostars. For the public version, visit https://www.biostars.org.
cptac data download

Hi friends

Is there any R code to download CPTAC data for a type of cancer?

rna-seq cptac
• 1,359 views • link
updated by Zhenyu Zhang Zhenyu Zhang • written by Rob • Rob

1 answer

Python code https://paynelab.github.io/cptac/

The genomic data are in GDC, and you can access via GenomicsDataCommons or TCGABiolinks.

• 0 views • link
written by Zhenyu Zhang Zhenyu Zhang

Log in to answer this question.

More posts like this
  • Mutation, MAF, CPTAC-3
    written by Rob • Rob
    Hi friends How can I download mutation data from CPTAC for kidney cancer (ccRCC)? Is there any R-code for this?
  • CPTAC data download
    written by Rob • Rob
    Hi friends Is there an R code to download CPTAC mutation data? I tried to use the following code but it did not work. I …
  • CPTAC data download, transcriptomics
    written by Rob • Rob
    Hi all, I am using python documentation to download the CPTAC data for ccRcc. I don't find anything about the type of data. I want …
  • HT-seq CPTAC,RNA-seq
    written by Rob • Rob
    Hi friends I am trying to download HT-seq CPTAC RNA-seq for kidney and there is no HT-seq in the workflow section. Instead there is star-count. …
  • CPTAC RNA seq
    written by Rob • Rob
    Hey friends I am using python code to download CPTAC transcriptomic data. But this is not raw count data. my code is : cptac.download(dataset="Ccrcc") transcriptomics …
  • CPTA, TCGA, RNA seq, validation
    written by Rob • Rob
    Hi friends Hope you all doing well. I want to validate my TCGA analysis with CPTAC transcriptomic data. I don't know why in the validation, …
  • plot, gene expression, RNA-seq
    written by Rob • Rob
    Hi friends I have a data file of gene expression, normalized. The first column is genes, the first raw is continuous values I want to …
  • RNA Seq HTSeq download GDC portal
    written by Rob • Rob
    Hi friends, I am trying to download ht-seq file form GDC portal but it gives me one file for each patients. Can you please let …
  • copy number variation analysis
    written by Rob • Rob
    Hi friends I want to do copy number variation analysis. How I can download gistic file for all lesions, deletion and amplification separately? what R …
  • HT-Seq count data coding gene
    written by Rob • Rob
    Hi friends I am using R code to download HT-Seq count data Does anybody know what line should I add to the code to download …