Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
https://github.com/seandavi/awesome-cancer-variant-databases
Last synced: 3 days ago
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Catalogs
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Germline
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GnomAD - The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. The data set provided on this website spans 123,136 exome sequences and 15,496 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies. [Web app, ?API, Download]
- dbSNP - [Web app, API, Download]
- Kaviar - Kaviar (~Known VARiants) is a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. Kaviar contains 162 million SNV sites (including 25M not in dbSNP) and incorporates data from 35 projects encompassing 77,781 individuals (13.2K whole genome, 64.6K exome). - [web app, API, Download]
- 1000 Genomes - [Web app, API, Download]
- ClinVar - [Web app, Download]
- Exome Sequencing Project - [Web app, Download]
- Genome of the Netherlands
- UK10K
- GEUVADIS: Genetic European Variation in Health and Disease
- SweGen - [Web app, API, Download]
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
- GEUVADIS: Genetic European Variation in Health and Disease
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Somatic
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Variant Effect Prediction tools and databases
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Germline
- CHASM
- CHASM
- fannsdb - Combines ConDEL and TransFIC annotations. FannsDB is a database for Functional ANnotations for Non Synonymous SNVs which contains precalculated scores for several predictors. [Web app, Download]
- dbNSFP - [Download]
- myvariant.info - [Web app, API]
- PolyPhen-2 - [Software tool, Download]
- SIFT
- MutationAssessor
- MutationTaster
- PROVEAN
- CADD
- GERP++
- PhyloP and PhastCons
- nsSNPAnalyzer
- SNPs&GO
- SNAP2
- SNPs3D
- MutPred2
- AUTO-MUTE
- Panther
- stSNP
- CoVEC
- CAROL
- CHASM
- CanDrA - 96 structural, evolutionary and gene features
- Kipoi - Kipoi is an API and a repository of ready-to-use trained models for genomics. It currently contains 2074 different models, covering canonical predictive tasks in transcriptional and post-transcriptional gene regulation. Kipoi's API is implemented as a python package and it is also accessible from the command line or R.
- CHASM
- CHASM
- CHASM
- CHASM
- CHASM
- CHASM
- CHASM
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Clinically-focused databases
- 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]
- 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]
- MyCancerGenome - My Cancer Genome is a personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers. My Cancer Genome gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. [web app, API, Download, *may require licensing*]
- OncoKB - OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions. [web app, API, Download]
- PharmGKB - PharmGKB is a comprehensive resource that curates knowledge about the impact
- Precision Medicine KnowledgeBase (PMKB) - PMKB is organized to provide information about clinical cancer variants and interpretations in a structured way, as well as allowing users to submit and edit existing entries for continued growth of the knowledgebase. All changes are reviewed by cancer pathologists. [web app, Download]
- 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]
- 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]
- CiViC - CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. [web app, API, Download]
- DGIdb - Mining the druggable genome for personalized medicine. [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]
- Molecular Oncology Almanac - A collection of putative alteration/action relationships identified in clinical, preclinical, and inferential studies from the VanAllen lab in Dana-Farber Cancer Institute. Described by Reardon, B., Moore, N.D., Moore, N.S. et al. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat Cancer 2, 1102–1112 (2021). https://doi.org/10.1038/s43018-021-00243-3. The MOAlmanac database, tools and app are available on their [github](https://github.com/vanallenlab/moalmanac-db)
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