nichenet-python

Python nichenetr package — modeling intercellular communication by linking ligands to target genes.

Installation

pip install nichenet-python                # from PyPI

For local development:

git clone https://github.com/Bio-Babel/Nichenet-python.git
cd Nichenet-python
pip install -e ".[dev]"

Runnable notebooks reproducing the R nichenetr vignettes live under tutorials/:

Notebook	Topic
`ligand_activity_geneset.ipynb`	Ligand activity analysis on a gene set of interest
`ligand_activity_single_cell.ipynb`	Per-cell ligand activity prediction
`ligand_target_signaling_path.ipynb`	Inferring ligand→target signaling paths
`target_prediction_evaluation_geneset.ipynb`	Evaluating target gene predictions
`seurat_steps.ipynb`	Step-by-step NicheNet analysis on a Seurat-style object
`seurat_steps_prioritization.ipynb`	Adds the prioritization scheme on top of `seurat_steps`
`seurat_wrapper.ipynb`	One-call wrapper for the Seurat-style workflow
`seurat_wrapper_circos.ipynb`	Wrapper workflow with circos visualization
`circos.ipynb`	Standalone circos plots of ligand→target / ligand→receptor links

pip install -e ".[docs]"
mkdocs serve

GPL-3.0-only, matching the upstream R nichenetr.

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

Source distribution for nichenet-python 2.2.1.1
File	Size	Uploaded
nichenet_python-2.2.1.1.tar.gz	5.1 MB	May 21, 2026	Details

Table of built distributions (wheels) for nichenet-python 2.2.1.1
File	Interpreter	ABI	Platform	Reset
nichenet_python-2.2.1.1-py3-none-any.whl 5.1 MB May 21, 2026	Python 3	none	any	Details

Total release size: 10.2 MB

Download URL	nichenet_python-2.2.1.1.tar.gz
Size	5.1 MB
Tags	Source
SHA-256 checksum How to use checksums	`f8dcd4d629091f857a46e6106b3cefac4235cd4ad2838a691b823c5a96b42e23`
BLAKE2b-256 checksum How to use checksums	`b9827b4034e7bb0855adc729ea930f2cb32c5dcf4a5e047eb7a0b379a4a5bffe`
Upload date	May 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.11.15`

Download URL	nichenet_python-2.2.1.1-py3-none-any.whl
Size	5.1 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`18e493c3999af80847d739779539b5d95b04d8608905a7d3b1bb711c964dc10d`
BLAKE2b-256 checksum How to use checksums	`79ce05e39a24098510db4575617080ea69bd0ba14ef5920897a2a0067809bd5e`
Upload date	May 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.11.15`

This release

2.2.1.1 This release