decoupler

Name	decoupler JSON
Version	2.1.1 JSON
	download
home_page	None
Summary	Python package to perform enrichment analysis from omics data.
upload_time	2025-07-18 05:11:41
maintainer	None
docs_url	None
author	Pau Badia i Mompel
requires_python	>=3.10
license	BSD 3-Clause License Copyright (c) 2025, scverse® Copyright (c) 2025, Pau Badia i Mompel, Saez lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
keywords
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # decoupler - Ensemble of methods to infer enrichment scores
<img src="https://raw.githubusercontent.com/scverse/decoupler/refs/heads/2.0.8/docs/_static/images/logo.svg" align="right" width="120" class="no-scaled-link" />


[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[![Issues][badge-issues]][issue tracker]
[![Coverage][badge-coverage]][codecoverage]
[![Stars][badge-stars]](https://github.com/scverse/anndata/stargazers)

[![PyPI][badge-pypi]][pypi]
[![Downloads month][badge-mdown]][down]
[![Downloads all][badge-adown]][down]

[![Conda version][badge-condav]][conda]
[![Conda downloads][badge-condad]][conda]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/decoupler/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/decoupler
[badge-condav]: https://img.shields.io/conda/vn/conda-forge/decoupler-py.svg
[badge-condad]: https://img.shields.io/conda/dn/conda-forge/decoupler-py.svg
[badge-issues]: https://img.shields.io/github/issues/scverse/decoupler
[badge-coverage]: https://codecov.io/gh/scverse/decoupler/branch/main/graph/badge.svg
[badge-pypi]: https://img.shields.io/pypi/v/decoupler.svg
[badge-mdown]: https://static.pepy.tech/badge/decoupler/month
[badge-adown]: https://static.pepy.tech/badge/decoupler
[badge-stars]: https://img.shields.io/github/stars/scverse/decoupler?style=flat&logo=github&color=yellow

`decoupler` is a python package containing different enrichment statistical
methods to extract biologically driven scores
from omics data within a unified framework. This is its faster and memory efficient Python implementation,
a deprecated version in R can be found [here](https://github.com/saezlab/decoupler).

[//]: # (numfocus-fiscal-sponsor-attribution)

decoupler is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

<div align="center">
<a href="https://numfocus.org/project/scverse">
  <img
    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
    width="200"
  >
</a>
</div>

## Getting started

Please refer to the [documentation][],
in particular, the [API documentation][].

## Installation

You need to have Python 3.10 or newer installed on your system.
If you don't have Python installed, we recommend installing [uv][].

There are several alternative options to install decoupler:

1. Install the latest stable release from [PyPI][pypi] with minimal dependancies:

```bash
pip install decoupler
```

2. Install the latest stable full release from [PyPI][pypi] with extra dependancies:

```bash
pip install decoupler[full]
```

3. Install the latest stable version from [conda-forge][conda] using mamba or conda (pay attention to the `-py` suffix at the end):

```bash
mamba create -n=dcp conda-forge::decoupler-py
```

4. Install the latest development version:

```bash
pip install git+https://github.com/scverse/decoupler.git@main
```

## Release notes

See the [changelog][].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][].
If you found a bug, please use the [issue tracker][].

## Citation

> Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D.,
Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O.
and Saez-Rodriguez J. 2022. decoupleR: Ensemble of computational methods
to infer biological activities from omics data. Bioinformatics Advances.
<https://doi.org/10.1093/bioadv/vbac016>

[uv]: https://github.com/astral-sh/uv
[scverse discourse]: https://discourse.scverse.org/
[scverse]: https://scverse.org/
[issue tracker]: https://github.com/scverse/decoupler/issues
[tests]: https://github.com/scverse/decoupler/actions/workflows/test.yaml
[documentation]: https://decoupler.readthedocs.io
[changelog]: https://decoupler.readthedocs.io/en/latest/changelog.html
[api documentation]: https://decoupler.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/decoupler
[down]: https://pepy.tech/project/decoupler
[conda]: https://anaconda.org/conda-forge/decoupler-py
[codecoverage]: https://codecov.io/gh/scverse/decoupler

            

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