crispr-screen

name	crispr-screen
description	CRISPR screen design & analysis (mirrors Claude Science's CRISPR screen skill). Designs guide libraries, runs enrichment/depletion analysis on read counts, and traces every hit back to its sgRNA support. Use for sgRNA libraries, screen counts, enrichment analysis.

crispr-screen

Guide design from genome annotation (connectors/ensembl.py); enrichment via MAGeCK or an equivalent Python implementation.

Standard workflow

1. Input sgRNA read-count table (inputs/).
2. Normalize + differential enrichment (median-ratio / RRA) + FDR; write script to outputs/.
3. Output ranked hit table + volcano/rank figures (figure-maker, saved to outputs/).
4. Attach each significant gene's supporting sgRNAs and statistics.

Hard rules

• State thresholds (FDR, logFC) and the control-group definition explicitly; no orphan hits (reviewer checks).