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MAGeCK CRISPR Screen Analysis

Analyzes pooled CRISPR screen read counts to rank gene hits with QC and FDR

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
4 files

What it does

Once installed, the agent can take pooled CRISPR knockout, CRISPRi, or CRISPRa screen data (raw sequencing reads or existing guide-count tables) and run the MAGeCK analysis workflow. It checks the guide library and sample layout, runs quality-control checks on replicates and read distribution, and ranks genes by enrichment or depletion with effect sizes and false discovery rates. It is designed to warn about weak inference rather than overstate results, and it does not design guides or look up public dependency scores.

Great for

  • Bioinformatics or wet-lab researchers analyzing their own pooled CRISPR screen data
  • Students learning how CRISPR screen statistics and quality control work
  • Developers building lab pipelines around MAGeCK 0.5.9.5

Skip it if

  • Looking up existing public gene essentiality scores (use DepMap instead), since this skill is for analyzing new screens
  • Clinical or diagnostic decisions, because gene hits from a screen alone do not establish gene function or therapeutic relevance
  • Users without MAGeCK 0.5.9.5 and NumPy/SciPy installed, since the analysis cannot run without those tools

Try asking

  • “Analyze my CRISPR knockout screen with these FASTQ files and a library TSV, comparing treated against control samples”
  • “Run QC on my guide count table and tell me which replicates correlate poorly”
  • “Rank hit genes from my count matrix at FDR 0.05 in both directions”
  • “Check whether my two-group contrast should be paired and validate the sample layout”
Step-by-step guide: how to use MAGeCK CRISPR Screen AnalysisInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 4 original files, the MIT licence and an attribution note.

    mageck.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip mageck.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip mageck.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Give explicit control and treatment sample groups and separate sequencing lanes from true biological replicates, since the helper will not guess the control group.
  • Rename numeric sample labels (for example with a prefix like c1) before analysis, because MAGeCK misreads plain numbers.
  • Review the QC output and MAGeCK's applied normalization method and warnings before trusting hit lists; treat the 10% zero and 0.8 correlation flags as prompts, not pass/fail rules.

What's inside

  • references/design.md
  • references/runtime.md
  • scripts/screen_analysis.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.