Biomedical datasets

There’s a lot of publicly accessible data out there, so why not keep a list to have them all handy? The best are sites that have nice interfaces but also allow you to easily download and handle the data. Here are some resources, in not yet logical order / organization.

Downloadable data tables:

GnomAD polymorphisms observed in genome / exome data.
GTEx RNAseq data. Download large data files, and search with Bash.
ClinVar of genetic variants.
depmap in cell lines.
cBioPortal genomics data
COSMIC of Somatic Mutations in Cancer
Genomics of Drug Sensitivity in Cancer specific sensitivities to compounds
NIH RePORTER on NIH-funded grants
Human Protein Atlas types of data about cells

Additional types of data:

Protein Data Bank structures
The Human Protein Atlas localization
Clinical Genome Resource information for genes
Genetic Testing Registry of approved genetic tests
EVcouplings coupling data
IntAct interactions
Timetree of organisms
PheWAS -wide association studies
FPbase proteins
PaxDb: Protein Abundance Database abundance (Mass Spec)
PEP Tracker Mass Spec
Gene Ontology Consortium / Protein associations
denovo-db of de novo variants seen in trios
DGIdbhttp://dgidb.orgDruggable targets?
Mouse Genome Informatics on genes (in mice)
Human Phenotype Ontogeny about the protein

Virus data:

HIV databases at Los Alamos National Labs genetic sequences and immunological epitopes
Virus Pathogen Resourcehttps://www.viprbrc.orgViral sequences (general)