pydeseq2
Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.
- Version
- 1.7
- License
- MIT license
- Compatibility
- Requires Python >=3.11 and PyDESeq2 0.5.4. Tested current stack uses Python 3.13 and AnnData 0.13.4 (which requires Python >=3.12). Local analyses need no credentials or network; installation and upstream example-data downloads need network access.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/pydeseq2/SKILL.md
- skills/pydeseq2/SKILL_CN.md
- skills/pydeseq2/references/analysis_patterns.md
- skills/pydeseq2/references/api_reference.md
- skills/pydeseq2/references/core_workflow_steps.md
- skills/pydeseq2/references/workflow_guide.md
- skills/pydeseq2/scripts/run_deseq2_analysis.py
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