Metadata-Version: 2.4
Name: singlecell-cookbook
Version: 0.2.2
Summary: A collection of tools for analyzing single-cell genomics data.
Project-URL: Homepage, https://github.com/aarriojas/singlecell-cookbook
Project-URL: Documentation, https://singlecell-cookbook.readthedocs.io
Project-URL: Repository, https://github.com/aarriojas/singlecell-cookbook
Project-URL: Issues, https://github.com/aarriojas/singlecell-cookbook/issues
Project-URL: Release Notes, https://github.com/aarriojas/singlecell-cookbook/releases
Author-email: Argenis Arriojas <arriojasmaldonado001@umb.edu>
License: MIT License
        
        Copyright (c) 2024 Argenis Arriojas
        
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License-File: LICENSE.md
Keywords: RNA-seq,analysis,bioinformatics,genomics,single-cell
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: <3.13,>=3.11
Requires-Dist: anndata
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scanpy
Requires-Dist: scipy
Provides-Extra: dev
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Requires-Dist: pre-commit~=4.0.1; extra == 'dev'
Requires-Dist: pytest~=8.3.3; extra == 'dev'
Requires-Dist: rpy2>=3.5.14; extra == 'dev'
Requires-Dist: ruff~=0.8.0; extra == 'dev'
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Provides-Extra: r
Requires-Dist: anndata2ri>=1.3; extra == 'r'
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Provides-Extra: test
Requires-Dist: pytest~=8.3.3; extra == 'test'
Description-Content-Type: text/markdown

# singlecell-cookbook

[![Tests](https://github.com/argearriojas/singlecell-cookbook/actions/workflows/tests.yml/badge.svg)](https://github.com/argearriojas/singlecell-cookbook/actions/workflows/tests.yml)

A collection of tools for analyzing single-cell genomics data.

## Installation

You can install the package using pip:

```bash
pip install singlecell-cookbook
```

For development installation:

```bash
git clone https://github.com/argearriojas/singlecell-cookbook.git
cd singlecell-cookbook
pip install -e ".[dev]"
```

### R Dependencies

Some features (like pseudobulk analysis) require R and specific R packages. To use these features:

1. Install the required R packages in R:

```R
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("edgeR", "MAST"))
```

2. Install the R dependencies in Python:

```bash
pip install "singlecell-cookbook[r]"
```

## Documentation

Documentation is available at [Read the Docs](https://singlecell-cookbook.readthedocs.io/).

## Development

To set up the development environment:

1. Clone the repository
2. Install development dependencies: `pip install -e ".[dev]"`
3. Install pre-commit hooks: `pre-commit install`

## License

TBD. We need to assess the license according to the imported packages.

## Author

Argenis Arriojas ([arriojasmaldonado001@umb.edu](mailto:arriojasmaldonado001@umb.edu))
