Python differential-expression

Open-source Python projects categorized as differential-expression
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Topics: rna-seq Python Snakemake sleuth sciworkflows
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Top 3 Python differential-expression Projects

  • PyDESeq2

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

    • Project mention: DESeq2 Normalization | /r/bioinformatics | 2023-06-09

    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.

  • diffexpr

    Porting DESeq2 into python via rpy2

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  • rna-seq-kallisto-sleuth

    A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Python differential-expression related posts

Index

What are some of the best open-source differential-expression projects in Python? This list will help you:

Project Stars
1 PyDESeq2 515
2 diffexpr 68
3 rna-seq-kallisto-sleuth 63

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