Scanpy ranked genes starter

Skill ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-ranked-genes-starter

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

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill scanpy-ranked-genes-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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Scanpy Ranked Genes Starter

Use this skill to run a deterministic toy differential-expression pass with Scanpy and extract top marker genes per group from a small count matrix.

What it does

Loads a toy count matrix and per-cell group labels.
Normalizes counts, log-transforms the matrix, and runs scanpy.tl.rank_genes_groups.
Returns compact JSON with top ranked genes for each group.

When to use it

You need a minimal, local, verified Scanpy starter beyond QC.
You want a template for marker ranking or toy single-cell differential-expression checks.

Inputs

--input: tab-separated count matrix
--groups: tab-separated cell/group labels
--method: Scanpy ranking method, default t-test
--top-n: number of genes per group, default 3
--out: optional JSON output path

Example

slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-ranked-genes-starter/scripts/run_scanpy_ranked_genes.py \
  --input skills/transcriptomics/scanpy-ranked-genes-starter/examples/toy_counts.tsv \
  --groups skills/transcriptomics/scanpy-ranked-genes-starter/examples/toy_groups.tsv \
  --top-n 2 \
  --out scratch/scanpy-ranked-genes/summary.json

Verification

Skill-local tests: python3 -m unittest discover -s skills/transcriptomics/scanpy-ranked-genes-starter/tests -p 'test_*.py'
Repository smoke: python3 -m unittest tests.smoke.test_local_skills -v