PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. (by owkin)
Add to my DEV experience Bioinformatics differential-expression Python rna-seq Transcriptomics
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pydeseq2.readthedocs.io
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PyDESeq2 reviews and mentions

Posts with mentions or reviews of PyDESeq2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-02-07.
  • DESeq2 Normalization
    1 project | /r/bioinformatics | 9 Jun 2023
    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.
  • When would you use R instead of Python?
    2 projects | /r/bioinformatics | 7 Feb 2023
    PyDESeq2? https://github.com/owkin/PyDESeq2

Stats

Basic PyDESeq2 repo stats
2
510
8.4
3 days ago

owkin/PyDESeq2 is an open source project licensed under MIT License which is an OSI approved license.

The primary programming language of PyDESeq2 is Python.

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