crispr-screen-analysis
CommunityIdentify CRISPR screen hits with MAGeCK.
AuthorMDhewei
Version1.0.0
Installs0
System Documentation
What problem does it solve?
CRISPR Screen Analysis (MAGeCK) automates end-to-end analysis of CRISPR pooled screens, turning raw counts or FASTQ-derived data into ranked gene hits and publication-quality figures.
Core Features & Use Cases
- Accepts a count table or FASTQ inputs plus sgRNA library and optional design matrix for multi-condition experiments.
- Supports MAGeCK test, MAGeCK mle, and full count-to-result pipelines (count, test, mle, all) and outputs gene-level and sgRNA-level summaries, volcano plots, rank plots, hit summaries, QC plots, and a metadata file.
- Handles MAGeCK availability with a Python-based RRA fallback to ensure results are always produced, and generates a complete figure suite for publication.
Quick Start
Run the analysis from a count table (with treatment and control groups) or FASTQ inputs to generate gene hits, plots, and a metadata file.
Dependency Matrix
Required Modules
magecknumpypandasmatplotlibscipystatsmodels
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: crispr-screen-analysis Download link: https://github.com/MDhewei/bioinfor-claw/archive/main.zip#crispr-screen-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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