Description
depmap is an agent skill for retrieving and analysing Cancer Dependency Map release data. DepMap integrates CRISPR screens from the Broad and Sanger institutes and hosts independent RNAi and drug-screen datasets. The skill covers CRISPR Chronos gene effects, cancer model annotations, omics biomarkers and PRISM compound response. You can use it to rank dependencies in cancer models, compare biomarker cohorts that you have specified in advance, look at co-essentiality, or relate genetic dependencies to compound response. The skill is clear that these analyses generate hypotheses, including target and synthetic-lethality hypotheses, and do not show clinical efficacy, a therapeutic window or a causal interaction. It also explains that RNAi, with DEMETER2, is a different perturbation method rather than an older way of scoring CRISPR data, so each question must be matched to its assay and a pinned release. The skill starts by discovering the current release and obtaining its files from the DepMap downloads page, and it reads the release notes.…
Highlights
- Ranks dependencies in cancer models
- CRISPR Chronos gene effects and PRISM response
- Compares prespecified biomarker cohorts
- Explains assay and release matching
- Hypotheses, not clinical claims
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depmap FAQ
What is DepMap?
The Cancer Dependency Map, which integrates CRISPR screens from Broad and Sanger and hosts RNAi and drug-screen datasets.
What can the skill do?
Rank dependencies in cancer models, compare biomarker cohorts, examine co-essentiality, and relate genetic dependencies to PRISM compound response.
Do the results prove a treatment works?
No. The skill says they generate hypotheses and do not establish clinical efficacy, a therapeutic window or a causal interaction.
Is RNAi the same as CRISPR scoring?
No. The skill says DEMETER2 scores RNAi, which is a different perturbation modality.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill depmap.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best depmap alternatives?
Popular alternatives to depmap include gget, biopython and bulk-rnaseq. See all depmap alternatives