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: 12 days ago
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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 (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-02-07T10:32:05.000Z (2 months ago)
• Last Synced: 2025-03-27T03:11:12.973Z (26 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: 83 MB
• Stars: 184
• Watchers: 5
• Forks: 27
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# decoupler - Ensemble of methods to infer biological activities 

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`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 single license, each original resource has its own. By default, `decoupler`

assumes an academic license, but commercial or nonprofit licenses can be specified in the `license` parameter of `decoupler`'s OmniPath functions.

[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.