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DepMap Cancer Dependency Analysis

Query and analyze Cancer Dependency Map release data for cancer gene dependencies and drug response

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

What it does

Once installed, the agent knows how to find and read release files from the Cancer Dependency Map (DepMap), a public research database of gene knockout screens in cancer cell lines. It can rank which genes cancer models depend on, compare biomarker groups, check whether genes behave together, and relate genetic dependencies to drug sensitivity data, while applying statistical checks and recording which release and checksum were used. Its outputs are hypotheses for further research, not evidence of clinical effect.

Great for

  • Cancer researchers exploring candidate gene targets or synthetic-lethality hypotheses
  • Bioinformatics students learning how DepMap files and identifiers are structured
  • Analysts who need reproducible, release-pinned DepMap analyses with recorded checksums

Skip it if

  • Clinical or treatment decisions, since the skill states its results do not establish clinical efficacy or a therapeutic window
  • Reading cancer data as proof of causal gene interactions, which the skill explicitly says it does not establish
  • Non-research users expecting a simple data download, since the workflow requires Python, statistics knowledge and possibly manual browser verification

Try asking

  • “Rank the genes most selectively required by lung adenocarcinoma cell lines compared with other cancer types using the latest DepMap Public release”
  • “Check whether two candidate genes are co-essential across cancer models”
  • “Compare CRISPR gene effect scores for a gene between models with and without a damaging mutation in a chosen gene”
  • “Relate a gene's dependency scores to PRISM drug sensitivity for a set of compounds”
Step-by-step guide: how to use DepMap Cancer Dependency AnalysisInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    depmap.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

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

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip depmap.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

  • Pin a specific DepMap release and keep the release name, retrieval date and local checksum with your outputs, since files change between releases
  • Use the README of each release to confirm units, identifier levels and default-entry flags before joining tables
  • Treat results as hypotheses and validate them with independent data or experiments before drawing conclusions

What's inside

  • references/dependency_analysis.md
  • scripts/depmap_data.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.