scanpy.pp.recipe_zheng17

scanpy.pp.recipe_zheng17(adata, *, n_top_genes=1000, log=True, plot=False, copy=False)

Normalize and filter as of Zheng et al. [2017].

Reproduces the preprocessing of Zheng et al. [2017] – the Cell Ranger R Kit of 10x Genomics.

Expects non-logarithmized data. If using logarithmized data, pass log=False.

Parameters:

adata AnnData

Annotated data matrix.

n_top_genes int (default: 1000)

Number of genes to keep.

log bool (default: True)

Take logarithm.

plot bool (default: False)

Show a plot of the gene dispersion vs. mean relation.

copy bool (default: False)

Return a copy of adata instead of updating it.

Return type:

AnnData | None

Returns:

Returns or updates adata depending on copy.