Find biological datasets, download files and read measurements with their metadata in Wolfram Language.
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Requires Wolfram Language 15.0 or later:
PacletInstall[ResourceObject["https://wolfr.am/1IzdEvymT"]]
Needs["WolframInstitute`BioDataLink`"]Find sources and build an accession link offline:
BioDataSourceSearch["protein", "Limit" -> 5][All, {"Prefix", "Name"}]
BioDataURL[{"pdb", "1CRN"}]Search GEO studies online:
BioDatasetQuery["GEO", "CRISPR AND Homo sapiens[Organism]", "PageSize" -> 3]Read the bundled counts for 2,700 human blood cells and 513 selected genes:
BioDatasetLoad[File[FileNameJoin[{PacletObject["WolframInstitute/BioDataLink"]["AssetLocation", "Examples"], "PBMC3k", "pbmc3k-subset.json"}]]]["ExpressionMatrix"]The computational essays explore expression, structures, genomes, rhythms and measurement uncertainty. Use the visualization functions with your own measurements.
Run make all for local validation. See CONTRIBUTING.md.
Code: MIT. Registry metadata and example data retain their own licenses. Cite BioDataLink and the original data sources.