scirpy.io.read_bracer

scirpy.io.read_bracer(path)

Read data from BraCeR ([LEM+18]).

Requires the changeodb.tab file as input which is created by the bracer summarise step.

Note

Reading data into Scirpy has the following constraints:

  • each cell can have up to four chains (Dual IR): two VJ and two VDJ chains.

  • Excess chains are removed (those with lowest read count/UMI count) and cells flagged as Multichain-cell.

  • non-productive chains are removed

  • chain loci must be IGMT locus names.

For more information, see Immune receptor (IR) model.

Parameters
path : str, PathUnion[str, Path]

Path to the changeodb.tab file.

Return type

AnnDataAnnData

Returns

AnnData object with BCR data in obs for each cell. For more details see Data structure.