decoupler - Ensemble of methods to infer biological activities

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.

For further information and example tutorials, please check our documentation.

If you have any question or problem do not hesitate to open an issue.

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 -c conda-forge -c bioconda decoupler

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 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 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