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]"

Tutorials

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

Documentation

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

License

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