Installation

Requirements

Python >= 3.10
numpy >= 1.23
scipy >= 1.9
pandas >= 1.5
anndata >= 0.8
statsmodels >= 0.14
patsy >= 0.5 (used for formula parsing)

From PyPI

Install pylimma from PyPI:

pip install pylimma

Optional extras:

pip install pylimma[plot]   # matplotlib for diagnostic plots
pip install pylimma[dev]    # pytest, ruff, mypy for running tests
pip install pylimma[docs]   # sphinx + nbsphinx for building docs

From source

git clone https://github.com/john-mulvey/pylimma.git
cd pylimma
pip install -e .[dev,plot]

R-parity testing

pylimma’s test suite is fixture-based - the CSV files in tests/fixtures/ are pre-computed by R limma and checked into the repository. Running pytest does not require an R installation.

Regenerating the fixtures (only needed if porting a new function or pulling a newer R limma version) does require R, Bioconductor limma, and the helper packages listed in Fixture-first validation strategy.