illico 0.3.0

Fast asymptotic mannwhitney-u test

illico

illico is a python library performing fast and lightweight wilcoxon rank-sum tests (same as scanpy.tl.rank_genes_groups(…, method="wilcoxon")), useful for single-cell RNASeq data analyses and processing. Approximate speed benchmarks ran on k562-essential can be found below.

Test	Format	illico	scanpy	pdex
OVO (reference="non-targeting")	Dense	~30s	~1h	~4h
OVO (reference="non-targeting")	Sparse	~30s	~1h30	~4h
OVR (reference=None)	Dense	~30s	~11h	X
OVR (reference=None)	Sparse	~30s	~10h	X

Installation

illico is compatible with python 3.11 and onward:

pip install illico -U

Getting started

The full documentation is available here. A simple starter could be:

import anndata as ad
from illico import asymptotic_wilcoxon

adata = ad.read_h5ad('dataset.h5ad') # (n_cells, n_genes)
de_genes = asymptotic_wilcoxon(
       adata,
       # layer="Y", # <-- If you want tests to run not on .X, but a specific layer
       group_keys="perturbation",
       reference=["non-targeting"|None], # <- `None` computes cluster-wise DE genes. Any other `str` will be interpreted as label of the control cells.
       is_log1p=[False|True], # <-- Specify if your data underwent log1p or not
       )

Release notes

See the changelog.

Why illico

The name illico is a wordplay inspired by the R package presto (now the Wilcoxon rank-sum test backend in Seurat). Aside from this naming reference, there is no affiliation or intended equivalence between the two. illico was developed independently, and although the statistical methodology may be similar, it was not designed to reproduce presto’s results.

Other tools available

1. scanpy also implements OVO and OVR asymptotic wilcoxon rank-sum tests.
2. pdex only implements OVO wilcoxon rank-sum tests.
3. As of December 2025, rapids-singlecell has a pending PR adding a rank_genes_groups feature. I could not benchmark this solution as I had no GPU available, but it is expected that it runs at least as fast as illico, because GPU-based.