cbioportal-database SKILL.md skillA
cbioportal-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/cbioportal-database@git:20260827.cbbeb75Pins git:20260827.cbbeb75 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/databases/cbioportal-database/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260827.cbbeb75, committed Aug 27, 2026
- First version recorded
- May 28, 2026
- Size
- 32,819 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# cBioPortal Database ## Overview cBioPortal for Cancer Genomics is a public repository of cancer genomics data including TCGA, ICGC, and hundreds of curated studies spanning 100+ cancer types. It provides somatic mutation profiles, copy number alterations (CNA), gene expression, clinical data (survival, stage, treatment history), and methylation data for tens of thousands of patient samples. Data is accessible via a REST API at `https://www.cbioportal.org/api/` with no authentication required. ## When to Use - Retrieving somatic mutation profiles (variant type, amino acid change) for a gene across TCGA studies - Querying copy number alteration data (amplification, deep deletion) for candidate cancer driver genes - Accessing clinical data — overall survival, disease-free survival, tumor stage — for survival curve analysis - Identifying which cancer studies have molecular profiling data for a specific cancer type (e.g., breast, lung) - Downloading gene expression (RNA-seq FPKM/RSEM) data from specific TCGA cohorts for differential expression analysis - Correlating genomic alterations with clinical outcomes in a specific study …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/cbioportal-database@sha256:f3d9fcf5a2faacb5The line at the top of this page pins the label git:20260827.cbbeb75, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_42vjpfpq4wduo5dp)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Aug 27, 2026, about one every 45 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260827.cbbeb75 latest | 2026-08-27 | cbbeb75 | 32,819 B | A | view · diff |
| git:20260528.0e69ced | 2026-05-28 | 0e69ced | 34,150 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 34,138 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (32819 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_42vjpfpq4wduo5dp GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/cbioportal-database GET https://markdownregistry.com/api/v1/blob/f3d9fcf5a2faacb5e45407ab1dedf7f2baf35031edd4425de900409ca023b611
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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