cbioportal-database
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.
npx skills add LeonChaoX/qinyan-academic-skills --skill cbioportal-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# cBioPortal Database ## Overview cBioPortal for Cancer Genomics (https://www.cbioportal.org/) is an open-access resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. It hosts data from The Cancer Genome Atlas (TCGA), AACR Project GENIE, MSK-IMPACT, and hundreds of other cancer studies — covering mutations, copy number alterations (CNA), structural variants, mRNA/protein expression, methylation, and clinical data for thousands of cancer samples. **Key resources:** - cBioPortal website: https://www.cbioportal.org/ - REST API: https://www.cbioportal.org/api/ - API docs (Swagger): https://www.cbioportal.org/api/swagger-ui/index.html - Python client: `bravado` or `requests` - GitHub: https://github.com/cBioPortal/cbioportal ## When to Use This Skill Use cBioPortal when: - **Mutation landscape**: What fraction of a cancer type has mutations in a specific gene? - **Oncogene/TSG validation**: Is a gene frequently mutated, amplified, or deleted in cancer? - **Co-mutation patterns**: Are mutations in gene A and gene B mutually exclusive or co-occurring? - **Survival analysis**: Do mutations in a gene associate with better or worse patient outcomes? - **Al
- Overview
- When to Use This Skill
- Core Capabilities
- 1. cBioPortal REST API
- 2. Browse Studies
- 3. Molecular Profiles
- 4. Mutation Data
- 5. Copy Number Alteration Data
- 6. Alteration Frequency (OncoPrint-style)
- 7. Clinical Data
- Query Workflows
- Workflow 1: Gene Alteration Profile in a Cancer Type
- Workflow 2: Pan-Cancer Gene Mutation Frequency
- Workflow 3: Survival Analysis by Mutation Status
Download TCGA BRCA data wget https://cbioportal-datahub.s3.amazonaws.com/brca_tcga.tar.gz
What does the cbioportal-database skill do?
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill cbioportal-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.