Metadata-Version: 2.4
Name: hormone2cell
Version: 0.1.1
Summary: A toolkit for predicting hormone producing and receiving strength in single cell datasets.
Home-page: https://github.com/Teichlab/hormone2cell
Author: Lijiang Fei, Krzysztof Polanskiu
Author-email: Lijiang Fei <lf529@cam.ac.uk>, Krzysztof Polanski <ktp27@cam.ac.uk>
License: MIT
Project-URL: Homepage, https://github.com/Teichlab/hormone2cell
Project-URL: Repository, https://github.com/Teichlab/hormone2cell
Project-URL: Issues, https://github.com/Teichlab/hormone2cell/issues
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scanpy
Requires-Dist: matplotlib-venn
Dynamic: author
Dynamic: home-page
Dynamic: license-file

# hormone2cell

**A toolkit for predicting hormone producing and receiving strength in single cell datasets.**

`hormone2cell` identifies hormone producing cell types (HPCs) and hormone receiving cell types (HRCs) from single-cell or single-nucleus expression data using a curated Hormone Receptor Reference Database. It applies cell-type-level expression filtering, multi-gene logic, and strength scoring to summarize predicted hormone production and reception across cell types.


<p align="center">
  <img src="docs/figures/hormone2cell_workflow_gptversion.png" alt="hormone2cell workflow" width="900">
</p>

<p align="center">
  <em>Overview of the hormone2cell workflow, created with AI assistance.</em>
</p>

## Installation

We recommend installing `hormone2cell` in a clean conda environment.

### Install from PyPI

```bash
# Create and activate conda environment
conda create -n hormone2cell_env python=3.10 -y
conda activate hormone2cell_env

# Install hormone2cell from PyPI
pip install hormone2cell
```

### Install from GitHub for development

If you want to install the latest development version from GitHub:

```bash
# Create and activate conda environment
conda create -n hormone2cell_env python=3.10 -y
conda activate hormone2cell_env

# Clone repository
git clone https://github.com/Teichlab/hormone2cell.git
cd hormone2cell

# Install in editable mode
pip install -e .
```

Alternatively, download the package via **Code → Download ZIP** from GitHub and install it locally:

```bash
cd hormone2cell
pip install -e .
```

## Usage and Documentation

**Function docstrings and package documentation** are available on the [ReadTheDocs page](https://hormone2cell.readthedocs.io/en/latest/).


**The detailed tutorial** is available as a [notebook](docs/Tutorial_pancreas.ipynb) and as a [rendered ReadTheDocs page](https://hormone2cell.readthedocs.io/en/latest/Tutorial_pancreas.html).


The **Hormone-Receptor Reference Database**, including gene definitions for each hormone and receptor, is available from the [Hormone Cell Atlas download page](https://hormonecellatlas.org.uk/accounts/downloads/file/table-s2b/).

## Other resources

For hormone-centric analyses and visualization, please visit the [Hormone Cell Atlas website](https://hormonecellatlas.org.uk/).

For the single-cell resource associated with this project, please visit the [Hormone Cell Atlas single-cell resource](https://hormonecellatlas.cellgeni.sanger.ac.uk/).

## Citation

Citation information will be added once available.

Parts of the method were informed by a previously published adaptive thresholding framework: [Nature Communications, 2024](https://www.nature.com/articles/s41467-024-46070-9).
