LN's $t$-test
Differential expression testing for single-cell transcriptomics with reduced false discoveries.
Installation
pip install ln-ttest
Usage
from lntest import rank_genes_groups_ln
rank_genes_groups_ln(adata, groupby="leiden", layer="norm_counts") # normalized, not log-transformed
adata.uns["rank_genes_groups"]["logfoldchanges"]
adata.uns["rank_genes_groups"]["lfc_se"]
Example
The notebook PBMC3k showcases LN's $t$-test finding much less DE genes than scanpy's $t$-test on the 3k PBMCS data set from 10x Genomics.
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