Metadata-Version: 2.1
Name: decoupler
Version: 1.7.0
Summary: Ensemble of methods to infer biological activities from omics data
Home-page: https://decoupler.readthedocs.io/
License: GPL-3.0-only
Keywords: systems biology,molecular biology,signaling network,transcriptomics,modeling,mechanistic modeling,activity inference,molecular network,omics,biomedicine,molecular footprint,molecular signature
Author: Pau Badia i Mompel
Author-email: pau.badia@uni-heidelberg.de
Requires-Python: >=3.9,<4.0
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numba (>=0.60.0,<0.61.0)
Requires-Dist: numpy (>=1,<2)
Requires-Dist: pandas (>=2.2.2,<3.0.0)
Requires-Dist: tqdm (>=4.66.4,<5.0.0)
Requires-Dist: typing-extensions (>=4.12.2,<5.0.0)
Project-URL: Bug Tracker, https://github.com/saezlab/decoupler-py/issues
Project-URL: Documentation, https://decoupler.readthedocs.io/
Project-URL: Repository, https://github.com/saezlab/decoupler-py
Description-Content-Type: text/markdown

# decoupler - Ensemble of methods to infer biological activities <img src="https://github.com/saezlab/decoupleR/blob/master/inst/figures/logo.svg?raw=1" align="right" width="120" class="no-scaled-link" />
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`decoupler` is a package containing different enrichment statistical methods to extract biological activities from omics data within a unified framework.
This is its faster and memory efficient Python implementation, for the R version go [here](https://github.com/saezlab/decoupleR).

For further information and example tutorials, please check our [documentation](https://decoupler-py.readthedocs.io/en/latest/index.html).

If you have any question or problem do not hesitate to open an [issue](https://github.com/saezlab/decoupler-py/issues).

## Installation

`decoupler` can be installed from `pip` (lightweight installation)::
```
pip install decoupler
```

It can also be installed from `conda` and `mamba` (this includes extra dependencies):
```
mamba create -n=decoupler conda-forge::decoupler-py
```

Alternatively, to stay up-to-date with the newest unreleased version, install from source: 
```
pip install git+https://github.com/saezlab/decoupler-py.git
```

## scverse
`decoupler` is part of the [scverse](https://scverse.org) ecosystem, a collection of tools for single-cell omics data analysis in python.
For more information check the link.

## License
Footprint methods inside decoupler can be used for academic or commercial purposes, except `viper` which holds a non-commercial license. 

The data redistributed by OmniPath does not have a license, each original resource carries their own. 
[Here](https://omnipathdb.org/info) one can find the license information of all the resources in OmniPath.

## 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>

