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Question: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
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gravatar for Ahdee
6 days ago by
Ahdee40
United States
Ahdee40 wrote:

Dear all, this is not a typical R question but I'm wondering if anyone knows a url or even a package that can download expected_counts for the TCGA data like LUAD.  I can easily download the rsem gene normalize dataset from places like firehose however I need to run a DGE using something like edgeR or Voom - limma that would require the counts instead.  Does anyone have a source? 

thanks. 

 

ADD COMMENTlink modified 6 days ago by Steve Lianoglou12k • written 6 days ago by Ahdee40
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gravatar for Steve Lianoglou
6 days ago by
Denali
Steve Lianoglou12k wrote:

Here are some options:

  1. Get the data from this paper, where the reprocessed the TCGA RNA-seq data using subread (GEO link).
  2. The recount project has a reprocessed version of the TCGA data. Click on the TCGA tab at the top there.
  3. The ARCHS4 project provides the "recount"ed TCGA data as and HDF5 file on its downloads page. This may be a more palatable way to consume the entire TCGA data, depending on how you plan on using it.
  4. The toil project has a subset of the TCGA data reprocessed using kallisto. You should be able to chase down a way to download the data from there, or from its listing on the kallisto site.
ADD COMMENTlink written 6 days ago by Steve Lianoglou12k

Steve, thanks, this is perfect.  the recount2 project looks awesome.  On top of that there is a R packages to make the download easier.  Found a great tutorial here in case anyone else is interested. 

https://www.bioconductor.org/packages/devel/workflows/vignettes/recountWorkflow/inst/doc/recount-workflow.html

ADD REPLYlink written 4 days ago by Ahdee40
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