sc-marker-extractor
CommunityReturn cluster marker genes as JSON for scRNA-seq
Data & Analytics#differential-expression#json-output#cluster-analysis#scrna-seq#marker-genes#cell-type-annotation
Authorya-way
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Extract cluster-level differential expression markers from clustered scRNA-seq data and return a machine-friendly JSON object for downstream interpretation and automation.
Core Features & Use Cases
- Per-cluster marker computation: computes differential markers for each cluster (Wilcoxon rank-sum) and outputs top markers per cluster.
- Structured JSON output: returns a JSON mapping of cluster IDs to ordered marker gene lists for easy programmatic consumption.
- Use case: annotate cell types or compare cluster markers across multiple scRNA-seq experiments.
Quick Start
Run the script with your clustered h5ad data to produce a markers.json file containing top markers per cluster.
Dependency Matrix
Required Modules
numpypandasscanpy
Components
scripts
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Please help me install this Skill: Name: sc-marker-extractor Download link: https://github.com/ya-way/cytoclaw-skills/archive/main.zip#sc-marker-extractor Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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