DESeq2 Normalization

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Bioinformatics differential-expression Python rna-seq

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  • PyDESeq2

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    • https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/preprocessing.py I'm not sure but only a normalized count matrix seems not enough to do differential expression analysis. For example, in this script, it gathers also the size factor from the raw read count matrix. Maybe you could find it somewhere or recalculate it.

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