LN's $t$-test
Differential expression testing on an asymptotically unbiased log-fold-change estimator.
Installation
pip install ln-ttest
From a checkout:
pip install -e .
Usage
from lntest import rank_genes_groups_ln
rank_genes_groups_ln(adata, groupby="leiden", layer="norm_counts")
adata.uns["rank_genes_groups"]["logfoldchanges"]
adata.uns["rank_genes_groups"]["lfc_se"] # SE of the LFC; lfc ± 1.96·se is the interval
Takes normalised, not log-transformed counts.
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