scirpy.io.read_bracer

scirpy.io.read_bracer(path, **kwargs)

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

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

Note

Since scirpy v0.13, there are no restrictions on the AIRR data that can be stored in the scirpy data structure, except that each receptor chain needs to be associated with a cell.

The scirpy Immune receptor (IR) model is now applied in later step using the index_chains() function.

For more information, see Storing AIRR rearrangement data in AnnData.

Parameters

path : str | PathUnion[str, Path]: Path to the changeodb.tab file.
**kwargs: are passed to from_airr_cells().

Return type

AnnData

Returns

AnnData object with AIRR data in obsm["airr"] for each cell. For more details see Storing AIRR rearrangement data in AnnData.