https://github.com/saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.
https://github.com/saezlab/decoupler-py

bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics

Last synced: 6 days ago
JSON representation

Python package to perform enrichment analysis from omics data.

• Host: GitHub
• URL: https://github.com/saezlab/decoupler-py
• Owner: saezlab
• License: gpl-3.0
• Created: 2021-11-16T13:22:35.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2025-01-17T13:45:33.000Z (18 days ago)
• Last Synced: 2025-01-17T14:53:37.554Z (18 days ago)
• Topics: bioinformatics, data-science, enrichment, enrichment-analysis, numba, python, single-cell, spatial-transcriptomics, transcriptomics
• Language: Python
• Homepage: https://decoupler-py.readthedocs.io/
• Size: 69.3 MB
• Stars: 176
• Watchers: 7
• Forks: 26
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# decoupler - Ensemble of methods to infer biological activities 

[![main](https://github.com/saezlab/decoupler-py/actions/workflows/ci.yml/badge.svg)](https://github.com/saezlab/decoupler-py/actions)

[![GitHub issues](https://img.shields.io/github/issues/saezlab/decoupler-py.svg)](https://github.com/saezlab/decoupler-py/issues/)

[![Downloads](https://static.pepy.tech/badge/decoupler)](https://pepy.tech/project/decoupler)

[![Documentation Status](https://readthedocs.org/projects/decoupler-py/badge/?version=latest)](https://decoupler-py.readthedocs.io/en/latest/?badge=latest)

[![codecov](https://codecov.io/gh/saezlab/decoupler-py/branch/main/graph/badge.svg?token=TM0P29KKN5)](https://codecov.io/gh/saezlab/decoupler-py)

[![Conda page](https://img.shields.io/conda/vn/conda-forge/decoupler-py.svg)](https://anaconda.org/conda-forge/decoupler-py)

[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/decoupler-py.svg)](https://anaconda.org/conda-forge/decoupler-py)

`decoupler` is a 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, 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

Enrichment 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.