depmap

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Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

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# DepMap — Cancer Dependency Map ## Overview The Cancer Dependency Map (DepMap) project, run by the Broad Institute, systematically characterizes genetic dependencies across hundreds of cancer cell lines using genome-wide CRISPR knockout screens (DepMap CRISPR), RNA interference (RNAi), and compound sensitivity assays (PRISM). DepMap data is essential for: - Identifying which genes are essential for specific cancer types - Finding cancer-selective dependencies (therapeutic targets) - Validating oncology drug targets - Discovering synthetic lethal interactions **Key resources:** - DepMap Portal: https://depmap.org/portal/ - DepMap data downloads: https://depmap.org/portal/download/all/ - Python package: `depmap` (or access via API/downloads) - API: https://depmap.org/portal/api/ ## When to Use This Skill Use DepMap when: - **Target validation**: Is a gene essential for survival in cancer cell lines with a specific mutation (e.g., KRAS-mutant)? - **Biomarker discovery**: What genomic features predict sensitivity to knockout of a gene? - **Synthetic lethality**: Find genes that are selectively essential when another gene is mutated/deleted - **Drug sensitivity**: What cell line features predict response to a compound? - **Pan-cancer essentiality**: Is a gene broadly essential across all cancer types (bad target) or selectively essential? - **Correlation analysis**: Which pairs of genes have correlated dependency profiles (co-essentiality)? ## Core Concepts ### Dependency...

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Author
K-Dense-AI
Repository
K-Dense-AI/scientific-agent-skills
Created
9 months ago
Last Updated
today
Language
Python
License
MIT

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Data & Documents Listed

depmap

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

13 Updated today
tassiovale
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depmap-crispr-essentiality

DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.

284 Updated 3 days ago
jaechang-hits
Data & Documents Listed

target-prioritization

Prioritize drug targets from a ranked gene list (e.g., scRNA-seq DE output) by orchestrating parallel API queries against UniProt, OpenTargets (with integrated DepMap CRISPR essentiality + gnomAD constraint), PubMed, the Human Protein Atlas (HPA), and ChEMBL tool compounds, then re-ranking by a composite score combining protein localization, druggability, disease genetics, tissue specificity (safety), focus-cell-type expression, CRISPR essentiality, LoF safety constraint, and research maturity. Use whenever the user wants to filter, triage, prioritize, or "do due diligence" on a list of candidate genes for drug discovery, especially after a DE / DEG analysis when they say things like "which of these should I follow up on", "filter for druggable targets", "make a target dossier", "rank these for tractability", "annotate these genes for druggability", or "build a target report". Trigger even when the user says just "filter these candidate genes" or hands over a CSV from a DE pipeline.

3 Updated 1 weeks ago
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