Metadata-Version: 2.4
Name: nichenet-python
Version: 2.2.1.1
Summary: Python nichenetr package — modeling intercellular communication by linking ligands to target genes.
Project-URL: Homepage, https://github.com/Bio-Babel/Nichenet-python
Project-URL: Repository, https://github.com/Bio-Babel/Nichenet-python
Project-URL: Issues, https://github.com/Bio-Babel/Nichenet-python/issues
Project-URL: Documentation, https://github.com/Bio-Babel/Nichenet-python#readme
Project-URL: Upstream (R package), https://github.com/saeyslab/nichenetr
Author-email: Jeffery Liu <jeffliu.lucky@gmail.com>
License-Expression: GPL-3.0-only
License-File: LICENSE
Keywords: R-port,cell-cell-interaction,intercellular-communication,ligand-receptor,ligand-target,nichenet,nichenetr,scRNA-seq,single-cell
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Typing :: Typed
Requires-Python: >=3.10
Requires-Dist: anndata>=0.10
Requires-Dist: matplotlib>=3.7
Requires-Dist: networkx>=3.0
Requires-Dist: numpy>=1.24
Requires-Dist: pandas>=2.0
Requires-Dist: pyarrow>=12.0
Requires-Dist: scanpy>=1.9
Requires-Dist: scikit-learn>=1.2
Requires-Dist: scipy>=1.10
Requires-Dist: seaborn>=0.12
Provides-Extra: circos
Requires-Dist: pycirclize>=1.0; extra == 'circos'
Provides-Extra: dev
Requires-Dist: build; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Requires-Dist: twine; extra == 'dev'
Provides-Extra: docs
Requires-Dist: mkdocs; extra == 'docs'
Requires-Dist: mkdocs-jupyter; extra == 'docs'
Requires-Dist: mkdocs-material; extra == 'docs'
Requires-Dist: mkdocstrings[python]; extra == 'docs'
Description-Content-Type: text/markdown

# nichenet-python

[![PyPI](https://img.shields.io/pypi/v/nichenet-python)](https://pypi.org/project/nichenet-python/)

Python [**nichenetr**](https://github.com/saeyslab/nichenetr) package — modeling intercellular communication by linking ligands to target genes.

## Installation

```bash
pip install nichenet-python                # from PyPI
```

For local development:

```bash
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/`](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

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

## License

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