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 (done on a 8-CPUs, 1 GPU machine) ran on k562-essential (~300k cells, 8k genes, 2k perturbations) can be found below.

Test Format illico scanpy pdex rapids-singlecell (GPU)
OVO (reference="non-targeting") Dense ~20s ~1h ~20min ~25min
OVO (reference="non-targeting") Sparse ~15s ~1h30min ~8min ~1h10min
OVR (reference=None) Dense ~10s >10h >10h ~1min
OVR (reference=None) Sparse ~10s >10h >10h ~1min

Installation

illico is compatible with python 3.11 and onward:

pip install illico -U

A dask extra is available if you wish to use dask.

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
       return_as_scanpy=[False|True], # <-- Whether to return a dict compatible with Scanpy's `rank_genes_groups` function, or a pd.DataFrame holding all p-values, statistics, and fold-change
       )
# Eventually, if return_as_scanpy=True:
adata.uns["rank_genes_groups"] = de_genes

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 also implements OVO and OVR wilcoxon rank-sum tests.
  3. As of March 2026, rapids-singlecell also implements OVO and OVR asymptotic wilcoxon rank-sum tests on GPU, with a focus on out-of-core datasets. If you are working with large datasets that do not fit in memory, you should check it out. For in-memory datasets, illico was benchmarked to be faster, even if CPU based.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for remydubois from gravatar.com remydubois

Credits

Author: remydubois

Requires

Python <4.0, >=3.11

Provides Extra

dask

Report project as malware

Metadata

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for remydubois from gravatar.com remydubois

Credits

Author: remydubois

Requires

Python <4.0, >=3.11

Provides Extra

dask

Report project as malware

Release files for illico 0.6.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for illico 0.6.0
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illico-0.6.0.tar.gz 428.7 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for illico 0.6.0
File
illico-0.6.0-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl 704.0 kB PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ x86-64 Details
illico-0.6.0-pp311-pypy311_pp73-musllinux_1_2_i686.whl 732.8 kB PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ x86-32 Details
illico-0.6.0-pp311-pypy311_pp73-musllinux_1_2_armv7l.whl 753.6 kB PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ ARMv7l Details
illico-0.6.0-pp311-pypy311_pp73-musllinux_1_2_aarch64.whl 655.9 kB PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ ARM64 Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 499.2 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl 515.1 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ IBM System/390x Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 656.6 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ PowerPC 64-le Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 478.6 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARMv7l Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 479.8 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARM64 Details
illico-0.6.0-pp311-pypy311_pp73-manylinux_2_5_i686.manylinux1_i686.whl 525.3 kB PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp315-cp315t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 492.4 kB CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp315-cp315t-manylinux_2_5_i686.manylinux1_i686.whl 514.2 kB CPython 3.15 CPython 3.15 free-threading Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp315-cp315-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 495.1 kB CPython 3.15 CPython 3.15 Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp315-cp315-manylinux_2_5_i686.manylinux1_i686.whl 519.4 kB CPython 3.15 CPython 3.15 Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp314-cp314t-musllinux_1_2_x86_64.whl 698.2 kB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details
illico-0.6.0-cp314-cp314t-musllinux_1_2_i686.whl 723.6 kB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-32 Details
illico-0.6.0-cp314-cp314t-musllinux_1_2_armv7l.whl 744.6 kB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARMv7l Details
illico-0.6.0-cp314-cp314t-musllinux_1_2_aarch64.whl 648.8 kB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details
illico-0.6.0-cp314-cp314t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 492.4 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp314-cp314t-manylinux_2_17_s390x.manylinux2014_s390x.whl 509.8 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ IBM System/390x Details
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illico-0.6.0-cp314-cp314t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 473.0 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARM64 Details
illico-0.6.0-cp314-cp314t-manylinux_2_5_i686.manylinux1_i686.whl 514.3 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp314-cp314-win_arm64.whl 321.9 kB CPython 3.14 CPython 3.14 Windows ARM64 Details
illico-0.6.0-cp314-cp314-win_amd64.whl 345.7 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
illico-0.6.0-cp314-cp314-musllinux_1_2_x86_64.whl 700.7 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
illico-0.6.0-cp314-cp314-musllinux_1_2_i686.whl 727.5 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-32 Details
illico-0.6.0-cp314-cp314-musllinux_1_2_armv7l.whl 747.6 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARMv7l Details
illico-0.6.0-cp314-cp314-musllinux_1_2_aarch64.whl 652.7 kB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
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illico-0.6.0-cp314-cp314-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 473.5 kB CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARMv7l Details
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illico-0.6.0-cp314-cp314-manylinux_2_5_i686.manylinux1_i686.whl 519.3 kB CPython 3.14 CPython 3.14 Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp314-cp314-macosx_11_0_arm64.whl 442.2 kB CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
illico-0.6.0-cp314-cp314-macosx_10_12_x86_64.whl 459.3 kB CPython 3.14 CPython 3.14 macOS 10.12+ x86-64 Details
illico-0.6.0-cp313-cp313-win_arm64.whl 321.4 kB CPython 3.13 CPython 3.13 Windows ARM64 Details
illico-0.6.0-cp313-cp313-win_amd64.whl 345.5 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
illico-0.6.0-cp313-cp313-win32.whl 317.5 kB CPython 3.13 CPython 3.13 Windows x86-32 Details
illico-0.6.0-cp313-cp313-musllinux_1_2_x86_64.whl 700.5 kB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
illico-0.6.0-cp313-cp313-musllinux_1_2_i686.whl 727.7 kB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-32 Details
illico-0.6.0-cp313-cp313-musllinux_1_2_armv7l.whl 747.4 kB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARMv7l Details
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illico-0.6.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 494.6 kB CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl 512.2 kB CPython 3.13 CPython 3.13 Linux glibc 2.17+ IBM System/390x Details
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illico-0.6.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 473.0 kB CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARMv7l Details
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illico-0.6.0-cp312-cp312-win_arm64.whl 322.0 kB CPython 3.12 CPython 3.12 Windows ARM64 Details
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illico-0.6.0-cp312-cp312-musllinux_1_2_x86_64.whl 701.5 kB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
illico-0.6.0-cp312-cp312-musllinux_1_2_i686.whl 728.2 kB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-32 Details
illico-0.6.0-cp312-cp312-musllinux_1_2_armv7l.whl 748.5 kB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARMv7l Details
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illico-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 496.4 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl 512.2 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ IBM System/390x Details
illico-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 650.2 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ PowerPC 64-le Details
illico-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 473.7 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARMv7l Details
illico-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 475.6 kB CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
illico-0.6.0-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl 520.3 kB CPython 3.12 CPython 3.12 Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp312-cp312-macosx_11_0_arm64.whl 441.5 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
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illico-0.6.0-cp311-cp311-win_amd64.whl 347.7 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
illico-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl 702.5 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
illico-0.6.0-cp311-cp311-musllinux_1_2_i686.whl 728.4 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-32 Details
illico-0.6.0-cp311-cp311-musllinux_1_2_armv7l.whl 752.6 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARMv7l Details
illico-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl 655.5 kB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
illico-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 497.8 kB CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
illico-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl 514.0 kB CPython 3.11 CPython 3.11 Linux glibc 2.17+ IBM System/390x Details
illico-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 655.7 kB CPython 3.11 CPython 3.11 Linux glibc 2.17+ PowerPC 64-le Details
illico-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 477.8 kB CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARMv7l Details
illico-0.6.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 479.5 kB CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
illico-0.6.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.whl 520.4 kB CPython 3.11 CPython 3.11 Linux glibc 2.5+ x86-32 Details
illico-0.6.0-cp311-cp311-macosx_11_0_arm64.whl 443.6 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
illico-0.6.0-cp311-cp311-macosx_10_12_x86_64.whl 460.3 kB CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details

Total release size: 44.5 MB

Release files / illico-0.6.0.tar.gz

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Release files / illico-0.6.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Release files / illico-0.6.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / illico-0.6.0-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.whl

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Release files / illico-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Release files / illico-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl

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Release files / illico-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl

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Release files / illico-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / illico-0.6.0-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl

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Release files / illico-0.6.0-cp312-cp312-macosx_11_0_arm64.whl

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Release files / illico-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl

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Release files / illico-0.6.0-cp311-cp311-musllinux_1_2_i686.whl

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Release files / illico-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / illico-0.6.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.whl

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Release files / illico-0.6.0-cp311-cp311-macosx_11_0_arm64.whl

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Release files / illico-0.6.0-cp311-cp311-macosx_10_12_x86_64.whl

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