scirpy.datasets.vdjdb

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scirpy.datasets.vdjdb#

scirpy.datasets.vdjdb(cached=True, *, cache_path='data/vdjdb.h5ad')#

Download VDJdb and process it into an AnnData object.

VDJdb [BVS+19] is a curated database of T-cell receptor (TCR) sequences with known antigen specificities.

Parameters:

  • cached (bool (default: True)) – If True, attempt to read from the data directory before downloading

  • cache_path (default: 'data/vdjdb.h5ad') – Location where the h5ad object will be saved

Return type:

AnnData

Returns:

An anndata object containing all entries from VDJDB in obsm["airr"]. Each entry is represented as if it was a cell, but without gene expression. Metadata is stored in adata.uns["DB"].

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