Pydeseq2 differential expression starter

Skill ma-compbio-lab/SkillFoundry/skills/transcriptomics/pydeseq2-differential-expression-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill pydeseq2-differential-expression-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

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PyDESeq2 Differential Expression Starter

Use this skill to run a deterministic toy bulk RNA-seq differential-expression pass with PyDESeq2 and summarize the ranked genes.

What it does

Loads a tiny count matrix and sample-condition table.
Fits a DESeq2-style model with PyDESeq2.
Runs the Wald test for the requested contrast.
Returns compact JSON with the top adjusted-p-value hits and effect sizes.

When to use it

You need a minimal local bulk RNA-seq differential-expression starter in Python.
You want a verified template for PyDESeq2 counts, metadata, and contrast handling.

Example

slurm/envs/transcriptomics/bin/python skills/transcriptomics/pydeseq2-differential-expression-starter/scripts/run_pydeseq2_differential_expression.py \
  --counts skills/transcriptomics/pydeseq2-differential-expression-starter/examples/toy_counts.tsv \
  --metadata skills/transcriptomics/pydeseq2-differential-expression-starter/examples/toy_metadata.tsv \
  --out scratch/pydeseq2/differential_expression_summary.json

Verification