DepMap (Claude Skill)

Claude skill for working with the Broad Institute’s Cancer Dependency Map data — genome-wide CRISPR knockout screens, RNAi, and compound-sensitivity assays across hundreds of cancer cell lines.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — actively maintained 2025–2026
Pricing Free / OSS skill; underlying DepMap data is publicly licensed
Capabilities Read-only — pulls and analyses public DepMap files

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/databases/depmap-crispr-essentiality into ~/.claude/skills/).
  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the depmap skill when prompted (also works in Cursor/Codex via the Agent Skills spec; requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/depmap ~/.claude/skills/

What it does

  • Identifies cancer cell lines by DepMap ID (cell-line names are ambiguous)
  • Downloads and analyses standard DepMap files locally: CRISPRGeneEffect.csv, OmicsExpressionProteinCodingGenesTPMLogp1.csv, OmicsSomaticMutationsMatrixDamaging.csv, OmicsCNGene.csv, sample_info.csv
  • Computes biomarker associations with multiple-testing correction
  • Adjusts for copy-number effects when interpreting essentiality scores

Primary use cases: Target validation (e.g., essentiality in KRAS-mutant lines), synthetic-lethal screening, biomarker discovery for oncology drug targets.

Notes

References Behan et al. 2019 (Nature, PMID 30971826) and Dempster et al. 2021 (Nature Methods, PMID 34349281) for methodology. Pulls files from the DepMap portal; large downloads are cached locally.

Sources

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