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bio-workflows-crispr-screen-pipeline

Automate CRISPR screen analysis from FASTQ data to hit genes.

Updated Mar 30, 2026
Search Tags:#workflow#analysis#screen#crispr#mageck#hit-calling
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-crispr-screen-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-workflows-crispr-screen-pipeline
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-wf-crispr-screen-pipeline
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-crispr-screen-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates the end-to-end analysis of pooled CRISPR screens, from raw FASTQ data through guide counting, QC, MAGeCK statistical testing, and hit calling, enabling researchers to identify candidate genes efficiently.

Core Features & Use Cases

  • End-to-end pipeline: from FASTQ to hit lists with multiple methods (MAGeCK, BAGEL2).
  • QC and replicate assessment to ensure robust results.
  • Flexible designs: supports single or multi-condition experiments, including CRISPRi/CRISPRa, dropout and enrichment screens.
  • Generates plots and reports for easy interpretation.

Quick Start

Run the CRISPR screen pipeline on your pooled screen FASTQ data to generate guide counts, QC metrics, hit calls, and visualization outputs.

Frequently Asked Questions about bio-workflows-crispr-screen-pipeline

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate pooled CRISPR screen analysis from FASTQ to hit genes?▼

You can automate pooled CRISPR screen analysis end-to-end by processing raw FASTQ data through guide counting, QC, MAGeCK statistical testing, and multi-method hit calling to identify candidate genes.

Can I analyze CRISPRi and CRISPRa enrichment and dropout screens in one pipeline?▼

Yes, this CRISPR screen pipeline supports flexible designs for both CRISPRi and CRISPRa experiments, explicitly covering dropout and enrichment scenarios across single or multi-condition setups to identify hits.

What is the best way to perform MAGeCK analysis and hit calling for CRISPR screens?▼

The best way to perform MAGeCK analysis and hit calling is using an integrated pipeline that combines guide counting, QC, and multi-method hit calling with BAGEL2 to produce reproducible candidate gene lists.

Does this CRISPR screen pipeline include QC and replicate assessment for robust results?▼

Yes, the CRISPR screen pipeline performs QC and replicate assessment to ensure robust results, generating plots and reports for easy interpretation of the guide counts and hit calls.

How do I go from guide counting to visualization in CRISPR screen analysis?▼

You go from guide counting to visualization by running an end-to-end CRISPR screen pipeline that processes FASTQ data through MAGeCK analysis and hit calling, ultimately generating plots and reports.

Do I need multiple tools for CRISPR screen hit calling or can one pipeline handle it?▼

You do not need multiple separate tools; this pipeline handles CRISPR screen hit calling using multiple methods like MAGeCK and BAGEL2 alongside guide counting, QC, and visualization for complete reproducible results.

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