liana.testing.kang_2018

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liana.testing.kang_2018#

liana.testing.kang_2018()#

Utility function to load the data from Kang et al., 2018; GSE96583.

The data contains ~25k PBMCs cells from 8 pooled patient lupus samples, each before and after IFN-beta stimulation. Kang, H., Subramaniam, M., Targ, S. et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 36, 89–94 (2018). https://doi.org/10.1038/nbt.4042

The dataset was preprocessed for and is available via pertpy (theislab/pertpy; Heumos et al., In prep.).

Returns:

Returns a largely pre-processed AnnData object with the following attributes: Raw counts for ~25k cells; ~15k genes; 16 samples; 2 conditions.

Examples

This downloads ~200MB from figshare on first call (and caches it in the working directory), so it is not run here:

import liana as li

adata = li.testing.kang_2018()

The resulting object carries obs['sample'], obs['condition'], obs['patient'] and obs['cell_abbr'], and is the starting point of several tutorials.

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