pydeseq2
Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
- Version
- 1.4
- License
- MIT license
- Compatibility
- Requires Python >=3.11 and PyDESeq2 0.5.4-compatible dependencies. Examples target PyDESeq2 0.5.x, formulaic design strings, explicit contrasts, and uv-based installs.
Pinned to revision 70a605012eee, 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/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
Every link opens the file at its source, pinned to the revision this page describes.