LIANA+

Contents

LIANA+#

LIANA+ is an all-in-one framework for cell-cell communication. It adapts and extends existing methods and prior knowledge to single-cell, spatially-resolved and multi-modal data, on AnnData and MuData objects, and is part of the scverse ecosystem.

Overview of the analyses that LIANA+ supports
Installation

Install LIANA+ with pip, uv or conda, with or without the optional extras.

Installation
Quickstart

Infer ligand-receptor interactions in a dissociated single-cell dataset.

Steady-state Ligand-Receptor inference
Tutorials

A decision tree, and a runnable notebook for each type of data and question.

Tutorials
API reference

Every method, preprocessing step, resource, dataset and plot.

API
Discussion

Ask a question on the scverse forum.

https://discourse.scverse.org/
GitHub

Read the source, report a bug, or open a pull request.

https://github.com/scverse/liana

Citation#

Please cite the framework paper [DSF+24], and the 2022 benchmark [DTGR+22] if you use the methods or resources it compared:

@article{Dimitrov2024,
    author  = {Dimitrov, Daniel and Sch{\"a}fer, Philipp Sven Lars and Farr, Elias and Rodriguez-Mier, Pablo and Lobentanzer, Sebastian and Badia-i-Mompel, Pau and Dugourd, Aurelien and Tanevski, Jovan and Ramirez Flores, Ricardo Omar and Saez-Rodriguez, Julio},
    title   = {LIANA+ provides an all-in-one framework for cell--cell communication inference},
    journal = {Nature Cell Biology},
    year    = {2024},
    volume  = {26},
    number  = {9},
    pages   = {1613--1622},
    doi     = {10.1038/s41556-024-01469-w},
    url     = {https://doi.org/10.1038/s41556-024-01469-w}
}

@article{Dimitrov2022,
    author  = {Dimitrov, Daniel and T{\"u}rei, D{\'e}nes and Garrido-Rodriguez, Martin and Burmedi, Paul L. and Nagai, James S. and Boys, Charlotte and Ramirez Flores, Ricardo O. and Kim, Hyojin and Szalai, Bence and Costa, Ivan G. and Valdeolivas, Alberto and Dugourd, Aur{\'e}lien and Saez-Rodriguez, Julio},
    title   = {Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data},
    journal = {Nature Communications},
    year    = {2022},
    volume  = {13},
    number  = {1},
    pages   = {3224},
    doi     = {10.1038/s41467-022-30755-0},
    url     = {https://doi.org/10.1038/s41467-022-30755-0}
}

Please also cite the individual methods and resources you relied on. Each method’s docstring names its original publication.

NumFOCUS#

LIANA+ is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

Contents