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depmap

Query DepMap Chronos CRISPR gene effect and PRISM sensitivity data for cancer dependency context.

Updated May 24, 2026
Search Tags:#cancer genomics#synthetic lethality#biomarker analysis#depmap#gene dependency#drug sensitivity#crispr chronos
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill depmap-estrella-231
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: depmap
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/depmap
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill depmap-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

It helps researchers identify cancer-specific gene dependencies and candidate drug targets by querying DepMap’s CRISPR dependency scores, gene effect profiles, and related annotation data.

Core Features & Use Cases

  • Cancer dependency lookup: Retrieve gene dependency scores (e.g., Chronos-based) across cancer cell lines for a target gene.
  • Selective vulnerability discovery: Compare dependency signals across cancer types/lineages to find selectively essential genes versus pan-essential “bad targets”.
  • Oncology validation & prioritization: Support synthetic lethality hypothesis generation and biomarker-style association checks between genomic features and drug or target sensitivity.

Quick Start

Use the depmap skill to evaluate whether gene KRAS shows cancer-lineage-selective dependency using DepMap Chronos gene effect scores and sample annotations.

Frequently Asked Questions about depmap

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find cancer-specific gene dependencies using DepMap CRISPR data?▼

You can retrieve gene dependency scores using DepMap Chronos gene effect data and sample annotations to compare dependency signals across cancer types and identify selectively essential genes.

What is synthetic lethality exploration with DepMap cell line data?▼

Synthetic lethality exploration uses DepMap matched cell lines to identify co-essentiality patterns and genomic biomarkers, generating hypotheses for cancer-selective vulnerabilities and target validation.

Can I use PRISM drug sensitivity data for biomarker discovery in cancer cell lines?▼

Yes, PRISM drug sensitivity files combined with cell line annotations support biomarker-style association checks between genomic features and drug sensitivity for oncology target prioritization.

Do I need to download DepMap CSV datasets like CRISPRGeneEffect.csv to analyze gene dependency?▼

Yes, you need either DepMap portal API access or downloaded CSV datasets like CRISPRGeneEffect.csv and sample_info.csv to perform thresholding and statistical validation for gene dependency analysis.

What's the best way to distinguish pan-essential bad targets from cancer-selective dependencies in DepMap?▼

Compare Chronos gene effect dependency signals across cancer lineages using sample annotations to distinguish selectively essential genes from pan-essential bad targets for oncology validation.

Does DepMap gene dependency analysis require statistical validation for target prioritization?▼

Yes, appropriate thresholding and statistical validation are required when analyzing DepMap gene dependency data to ensure reliable target prioritization and synthetic lethality hypothesis generation.

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