cellbender.py

Overview

This module contains helper functions for pipeline_cellbender.py

cellhub.tasks.cellbender.anndata_from_h5(file: str, analyzed_barcodes_only: bool = True) AnnData

Load an output h5 file into an AnnData object for downstream work.

Parameters:
  • file – The h5 file

  • analyzed_barcodes_only – False to load all barcodes, so that the size of the AnnData object will match the size of the input raw count matrix. True to load a limited set of barcodes: only those analyzed by the algorithm. This allows relevant latent variables to be loaded properly into adata.obs and adata.obsm, rather than adata.uns.

Returns:

The anndata object, populated with inferred latent variables

and metadata.

Return type:

adata

cellhub.tasks.cellbender.dict_from_h5(file: str) Dict[str, ndarray]

Read in everything from an h5 file and put into a dictionary.