awesome-cancer-variant-resources

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

331

GitHub Stars

Curated Resources

Use this list with your AI agent

Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:

"Show me germline resources from awesome-cancer-variant-resources"

AlphaMissense
AI model developed by Google DeepMind that predicts the pathogenicity of every possible missense mutation in the human proteome (Cheng et al., 2023). The model builds on the protein structure prediction tool AlphaFold2 (Jumper et al., 2021) and uses predicted structural context and fine-tuning on weak labels from population frequency data to provide variant effect predictions at scale. R/Bioconductor interface:
AUTO-MUTE
CADD
CanDrA
96 structural, evolutionary and gene features
CAROL
CHASM

Cancer Genome Interpreter
designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. CGI relies on existing knowledge collected from several resources and on computational methods that annotate the alterations in a tumor according to distinct levels of evidence. [web app, API]
CanDL
an expert-curated database of potentially actionable driver mutations for molecular pathologists and laboratory directors to facilitate literature-based annotation of genomic testing of tumors. [web app, Download]
CiViC
CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. [web app, API, Download]
Database of Curated Mutations (DOCM)
DoCM, the Database of Curated Mutations, is a highly curated database of known, disease-causing mutations that provides easily explorable variant lists with direct links to source citations for easy verification. [web app, API, Download]
DGIdb
Mining the druggable genome for personalized medicine. [web app, API, Download]
JAX Lab Clinical Knowledge Base
The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. [web app]

PCGR
The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual cancer genomes for precision oncology. It interprets both somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl’s Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations retrieved flexibly through vcfanno, and produces interactive HTML reports intended for clinical interpretation. - [Software tool]
UNMIRI NGS interpretation API & schema
[API, Software tool]

Showing a sample of 53 resources. View the full list on GitHub →