pydeseq2
Turn RNA-seq counts into tested gene comparisons.
What it does
Analyze bulk RNA-seq counts to produce differential-expression tables, coefficient-matched effect estimates, and visualizations.
When to use it
Use for bulk RNA-seq analyses with biological replicates, covariates, and explicit comparisons, not single-cell per-cell testing.
How to use it
Give it count and sample-metadata files, an experimental design, and a comparison; it saves differential-expression results and fitted-model metadata.
What you provide
- the experimental design
- the comparison to test
- Your files
Uses
Good to know
- advertises something the task does not need
What you need · 6
Requires Python >=3.11; the documented tested stack uses Python 3.13, and its AnnData 0.13.4 requires Python >=3.12.
Requires PyDESeq2 0.5.4; the quick-start installation pins that version.
Access · 3
This skill
https://arxiv.org/abs/2609.00065
Checks the current citation record
pydeseq2
Installs PyDESeq2 in an isolated environment