depmap

Queries the DepMap database for gene dependency scores across cancer cell lines.

Updated Mar 10, 2026

Search Tags:#bioinformatics #cancer genomics #drug targets #depmap #gene dependency #crispr screens

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill depmap

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: depmap
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/depmap
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill depmap

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to the Cancer Dependency Map (DepMap) data, enabling researchers to identify genes essential for cancer cell survival and pinpoint potential therapeutic targets.

Core Features & Use Cases

Query Gene Dependencies: Retrieve CRISPR knockout scores for specific genes across hundreds of cancer cell lines.
Identify Selective Vulnerabilities: Find genes that are essential only in certain cancer types or subtypes.
Biomarker Discovery: Correlate gene essentiality with mutations, expression, or copy number alterations.
Use Case: Investigate if the gene 'KRAS' is selectively essential in lung cancer cell lines compared to other cancer types.

Quick Start

Use the depmap skill to find cell lines selectively dependent on the gene 'KRAS' within the 'Lung' cancer type.

Frequently Asked Questions about depmap

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

FAQPage Schema

How do I find cancer cell lines selectively dependent on a specific gene using CRISPR screens?▼

To find selectively dependent cell lines, query gene dependency scores from CRISPR Chronos screens across cancer cell lines. This identifies cancer-specific vulnerabilities by comparing gene essentiality profiles against cell line annotations to pinpoint selective dependencies.

What is the difference between CRISPR Chronos and RNAi data in cancer gene dependency screens?▼

CRISPR Chronos and RNAi represent different screening technologies for gene dependency. Querying both data types allows cross-validation of gene essentiality profiles, reducing off-target effects and confirming selective vulnerabilities across cancer cell lines.

Can I use DepMap data to identify synthetic lethal interactions for drug target validation?▼

Yes, you can analyze DepMap gene essentiality profiles to identify synthetic lethal interactions. By correlating gene dependency scores with mutations or copy number alterations, researchers can validate drug targets and discover biomarkers.

How do I retrieve gene dependency scores for large-scale bioinformatics research?▼

You can retrieve gene dependency scores via API for targeted queries or download datasets for local analysis. This programmatic access supports large-scale bioinformatics research by enabling batch processing of gene essentiality profiles across hundreds of cancer cell lines.

Does DepMap support correlating gene essentiality with cancer mutations and copy number alterations?▼

Yes, DepMap supports biomarker discovery by correlating gene essentiality with mutations, expression, or copy number alterations. This facilitates identifying genes essential only in certain cancer types or subtypes by analyzing cell line annotations alongside dependency scores.