Building the GTEx tiledb database

[adomingues]

Building the GTEx tiledb database

[aaronwolen]

Thanks, @adomingues! Glad it was helpful!

I'll need to dig around for the original script as I built this several years ago. However, I can tell you it was written in Python and leveraged tiledb-py's from_pandas() method to create the array.

That said, we now have a much better solution for storing/querying this type of data using TileDB, called SOMA. This is a joint effort with the folks at CZI to create a scalable, language agnostic format for 'omics data, which now serves as the basis for the CZ CELLxGENE Discover Census. SOMA provides APIs in R and Python for interoperability with Seurat, AnnData/Scanpy, and, very soon, Bioc SummarizedExperiment/SingleCellExperiment.

Feel free to email me directly (my first name + @tiledb.com) if you'd like to setup a call to learn more about it.