Installation

Installation#

Basic Installation#

Install LIANA using pip:

pip install liana

Conda Installation#

conda install bioconda::liana

Installation with Extras#

LIANA offers optional dependencies for extended functionality:

All Extras#

Install all optional dependencies:

pip install 'liana[extras]'

This includes additional packages for:

  • Multi-view analysis (decoupler, muon, mofax, mofapy2)

  • Database access (omnipath)

  • Differential expression (pydeseq2)

  • Pathway analysis (gseapy)

  • Optimization (corneto, cvxpy-base, PySCIPOpt)

  • And more (cell2cell, kneed)

Development Installation From Source#

git clone https://github.com/saezlab/liana-py.git
cd liana-py
pip install -e '.[dev]'

Requirements#

  • Python 3.10 or higher (up to 3.13)

  • Core dependencies: anndata, mudata, scanpy, numba, pandas, and others are installed automatically