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DepMap Cancer Dependency Analysis

A skill for querying and analyzing DepMap CRISPR gene dependency and drug sensitivity data to validate cancer-specific targets.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 7/10Last updated: Aug 9, 2026

What it does

  • Teaches Claude how to work with the Broad Institute's DepMap resources: CRISPR Chronos gene effect scores, RNAi (DEMETER2), and PRISM compound sensitivity.
  • Documents score interpretation thresholds (Chronos ≤ −0.5 dependent, ≤ −1 strongly dependent) and cell-line metadata fields (DepMap_ID, lineage, primary_disease).
  • Ships Python snippets for selective-dependency discovery, mutation↔dependency biomarker testing (Mann–Whitney), and co-essentiality correlation.
  • Includes three workflows (target validation by cancer type, synthetic lethality screening, compound sensitivity) plus a reference table of key data files.

Who it's for

  • Oncology drug-discovery and translational researchers validating targets.
  • Bioinformaticians working with cancer functional genomics data.
  • Graduate researchers who must separate pan-essential genes from cancer-selective dependencies.

Example uses

  1. "Is gene X essential in KRAS-mutant lung lines?" → filter cell lines, compare gene effect vs. other lineages.
  2. "Find synthetic lethal partners in BRCA1-mutant lines" → mutant vs. WT comparison with FDR correction.
  3. "List the top 20 genes whose dependency profile correlates with gene X" → co-essentiality analysis to infer complexes or pathways.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/depmap/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/depmap folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/depmap/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/depmap ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal.
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r scientific-agent-skills/skills/depmap ~/.claude/skills/
  5. Install Python dependencies: pip install pandas numpy scipy requests
  6. Download the data files you need (CRISPRGeneEffect.csv, sample_info.csv, PRISM files) from https://depmap.org/portal/download/all/ into your working directory.
  7. Restart Claude Code and prompt something like "Use DepMap to check whether this gene is a selective dependency in pancreatic cancer lines."
View source on GitHub ↗License: MIT