Using TCGABioLinks to query multiple cancer studies
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Entering edit mode
11 weeks ago
ivykosater • 0

I have a list of cancer samples that I wish to download transcriptome data for using TCGABiolinks. I use the GDCquery() function for downloading data, however my list spans multiple TCGA projects. Here is my code

query <- GDCquery(project = "", data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts",
                  barcode = acc_numbers)

I am unsure what to put in the project argument. I do not think there is an argument for the TCGA pan cancer atlas, so does anyone know what I should do here?

RNA-Seq R TCGA • 139 views
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