alterlab-cosmic
From the author
Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cosmic -a claude-code
Installs to .claude/skills/alterlab-cosmic/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
Want your agent to suggest skills while you type? See how to use skills from your IDE.
Safety checks on SKILL.md
- Ships scripts we have not reviewedLow
Why 77
aiqbench computes the trust score from public signals. It is not a security audit, so read a skill before you install it.
Similar skills
Closest to this one by what they do and when they are used.
- cosmic-databasejaechang-hits/SciAgent-SkillsQuery COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.Data★ 383
- alterlab-clinvarAlterLab-IEU/AlterLab-Academic-SkillsQuery NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-depmapAlterLab-IEU/AlterLab-Academic-SkillsQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.Security★ 78
- alterlab-imaging-data-commonsAlterLab-IEU/AlterLab-Academic-SkillsQuery and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale radiology (CT, MR, PET) or digital pathology DICOM datasets for AI/ML training or cancer imaging research. Part of the AlterLab Academic Skills suite.Browser★ 78
- alterlab-geoAlterLab-IEU/AlterLab-Academic-SkillsAccess NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-matchmsAlterLab-IEU/AlterLab-Academic-SkillsComputes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use alterlab-pyopenms. Part of the AlterLab Academic Skills suite.Planning★ 78
Ratings & reviews
—
no reviews
Tried this skill? Rate it to help others. Sign in
Discussion
Join the discussion. Sign in