OmicIDX

SRA, GEO, BioSample, BioProject, and PubMed metadata as Parquet files you can query from DuckDB, Python, or R. Rebuilt nightly. No account, no key.

Get the data Try it in your browser View on GitHub

-- DuckDB: no download, no credentials
ATTACH 'https://omicidx.cancerdatasci.org/data/latest/omicidx.duckdb' AS omicidx (READ_ONLY);
SELECT run_accession, study_title FROM omicidx.sradb.rnaseq_runs WHERE taxon_id = 9606 LIMIT 10;

Displaying records 1 - 10

run_accession	study_title
DRR391952	Spatial transcriptome analysis of human oral cancers
DRR391953	Spatial transcriptome analysis of human oral cancers
DRR391954	Spatial transcriptome analysis of human oral cancers
DRR391955	Spatial transcriptome analysis of human oral cancers
DRR391969	Transcriptome analysis of human gingival epithelial cells treated with short-chain fatty acids
DRR391970	Transcriptome analysis of human gingival epithelial cells treated with short-chain fatty acids
DRR391971	Transcriptome analysis of human gingival epithelial cells treated with short-chain fatty acids
DRR394097	Single Cell RNA sequence of clinical breast cancer stem-like cells
DRR394098	Single Cell RNA sequence of clinical breast cancer stem-like cells
DRR394099	Single Cell RNA sequence of clinical breast cancer stem-like cells

Get the data

Everything lives under https://omicidx.cancerdatasci.org/data/. Query it in place with DuckDB, or use the Python and R recipes. Releases lists every version, its tables and sizes.

Use it from R

The omicidxr package connects in one line, pins a version, and replaces SRAdb and GEOmetadb.

Cite a release

Monthly releases on HuggingFace carry a git tag and a DOI. Download one and query it locally. See Versions and citation.

Try it in your browser

The playground runs SQL against latest/ with DuckDB-Wasm, and every SQL example in these docs opens in the DuckDB Shell. Nothing to install.

New here? Read what OmicIDX is, the sources it indexes, and how it’s built.