alterlab-pydeseq2
byalterlab-ieu· 90 skills
Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.
How to install alterlab-pydeseq2?
alterlab-ieu/alterlab-academic-skills/alterlab-pydeseq2
$npx -y skills add alterlab-ieu/alterlab-academic-skills --skill alterlab-pydeseq2Installs into the current project.
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Run `npx skills use "https://github.com/alterlab-ieu/alterlab-academic-skills" --skill "alterlab-ieu/alterlab-academic-skills/alterlab-pydeseq2"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/alterlab-ieu/alterlab-academic-skills" that are relevant to the current task. Run `npx skills add "https://github.com/alterlab-ieu/alterlab-academic-skills"` and select the relevant skills, then follow their instructions.
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