depmap-crispr-essentiality
DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.
npx skills add BioTender-max/awesome-bio-agent-skills --skill depmap-crispr-essentiality --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# DepMap CRISPR Gene Effect Analysis Guide ## Overview This guide covers the correct interpretation and analysis of DepMap CRISPR gene effect (Chronos) data. The most critical and common error in DepMap analyses is failing to negate the CRISPR scores when computing correlations with "essentiality." A secondary but equally damaging mistake is using bulk correlation shortcuts that mishandle per-gene NaN patterns. This guide provides the mandatory sign convention, the correct per-gene NaN-safe Spearman correlation implementation, and data loading/alignment procedures. ## Key Concepts ### DepMap CRISPR Score Convention The CRISPR gene effect score (produced by the Chronos algorithm) quantifies how gene knockout affects cell viability: - **Negative score**: gene knockout reduces cell viability -- the gene is **essential** for that cell line - **Zero score**: no measurable effect on viability - **Positive score**: gene knockout increases viability (rare, may indicate tumor-suppressive behavior) The DepMap portal distributes these scores in the file `CRISPRGeneEffect.csv`. Each row is a cell line (DepMap ID, e.g., `ACH-000001`) and each column is a gene in the format `GENE_NAME (ENTREZ_ID
- Overview
- Key Concepts
- DepMap CRISPR Score Convention
- Essentiality Sign Interpretation
- Data Structure: CRISPRGeneEffect Format
- Decision Framework
- Best Practices
- Common Pitfalls
- Workflow
- Further Reading
- Related Skills
What does the depmap-crispr-essentiality skill do?
DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill depmap-crispr-essentiality --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.