alterlab-depmap
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/data_page/
- Figshare deposits (programmatic, keyless): https://api.figshare.com/v2/articles/{article_id}
Access model — read this first. DepMap has no documented, stable public REST API for gene-level queries, and the portal (including depmap.org/portal/api/... and the data page) now sits behind a Cloudflare browser-verification check that asks users not to scrape it — scripted requests get the verification page, not data. The supported workflow is: download the release matrix CSVs, then analyse them locally with pandas. The keyless programmatic path to those files is the Figshare API for releases up to 24Q4 (/articles/{id}/files?page_size=1000 lists name + download_url; the endpoint is paginated, 10 files per page by default); scripts/query_depmap.py wraps this. Newer releases (25Q2 onward; latest 26Q1, April 2026) are downloaded in a browser from the data page. For Sanger's Project Score CRISPR screens there is a keyless JSON:API at https://api.cellmodelpassports.sanger.ac.uk (non-commercial use).