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mschubert / TCGAbiolinks-downloader Public

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TCGAbiolinks-downloader

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pproc_vst.r

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12 lines (8 loc) · 244 Bytes

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TCGAbiolinks-downloader

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pproc_vst.r

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12 lines (8 loc) · 244 Bytes

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library(SummarizedExperiment)

library(DESeq2)

INFILE = commandArgs(TRUE)[1]

OUTFILE = commandArgs(TRUE)[2]

data = readRDS(INFILE)

eset = DESeqDataSet(data, design=~1)

vst = varianceStabilizingTransformation(eset)

saveRDS(vst, file=OUTFILE)

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