DepMap Cancer Dependency Analysis
Query DepMap CRISPR gene dependency and drug sensitivity data to find cancer-selective vulnerabilities and validate oncology targets.
What it does
Gives Claude a working playbook for the Broad Institute's Cancer Dependency Map (DepMap): CRISPR Chronos gene effect scores, RNAi (DEMETER2) dependencies, and PRISM compound sensitivity. It defines how to read Chronos scores (≤ -0.5 likely dependent, ≤ -1 strongly dependent), explains cell-line metadata fields, and ships Python helpers for finding selective dependencies, testing mutation-based biomarker associations with Mann-Whitney, and computing co-essentiality correlations. A reference table maps the key download files (CRISPRGeneEffect.csv, sample_info.csv, OmicsCNGene.csv, PRISM data) plus best-practice caveats like copy-number and expression confounders.
Who it's for
- Drug discovery scientists validating oncology targets
- Cancer genomics researchers hunting synthetic lethal partners
- Grad students and bioinformaticians screening context-specific vulnerabilities
Example uses
- "Which genes are selectively essential in KRAS-mutant lung lines?" → compare gene effect between mutant and wild-type groups with significance testing.
- "Is my target pan-essential or cancer-selective?" → inspect distribution and variance across all lines to judge druggability.
- "Show the 20 genes most co-essential with my gene" → infer shared complexes or pathways from correlated dependency profiles.
· · · Install guide · · ·
Install in the Claude app (no terminal)
- Download the ZIP with the button below.
- In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
- Go to Customize → Skills → + → 'Upload a skill' and upload the 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.
- Open a terminal.
- Clone the repo:
git clone https://github.com/K-Dense-AI/scientific-agent-skills.git - Create the skills folder:
mkdir -p ~/.claude/skills - Copy just this skill:
cp -r scientific-agent-skills/skills/depmap ~/.claude/skills/ - Install Python deps:
pip install pandas numpy scipy requests - Download
CRISPRGeneEffect.csvandsample_info.csvfrom https://depmap.org/portal/download/all/ into your working directory (files can be hundreds of MB). - Restart Claude Code and prompt something like "use the depmap skill to analyze KRAS dependency in lung lines".