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gevaertlab / sequoia-pub

SEQUOIA: Digital profiling of cancer transcriptomes with grouped vision attention
https://sequoia.stanford.edu
MIT License
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Creating gene expression matrix for TCGA BRCA project #1

Open MarioPaps opened 2 months ago

MarioPaps commented 2 months ago

Hello,

Is there a chance you have access to the complete version of the 'ref.csv' file with normalised gene expression values for all patients in TCGA-BRCA project? Or do you know how to build this from TCGA tsv data?

YuanningEric commented 1 month ago

Hi, TCGAbiolink (https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html) is a handful tool to retrieve the gene expression data. Since the gene expression matrix is large, and we are not the legal owner for TCGA data, we do not provide those data matrices. Hopefully this is helpful!

MarioPaps commented 1 month ago

Hi, so did you follow the script in link 5. Mutation data?

I assume the matrix can be obtained from running one script?

I tried to build the matrix from the TCGA gene clustering tool, but it cannot export all the genes simultaneously-only 5 at a time.