fanzheng10 / decoupler

R package to infer biological activities from omics data using a collection of methods.

decoupleR

Overview

There are many methods that allow us to extract biological activities from omics data. decoupleR is a Bioconductor package containing different statistical methods to extract biological signatures from prior knowledge within a unified framework. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

For more information about how this package has been used with real data, please check the following links:

• decoupleR’s vignette
• Python implementation (Coming soon)
• decoupleR’s manuscript repository
• Creation of benchmarking pipelines
• Example of Kinase and TF activity estimation

Installation

decoupleR is an R package distributed as part of the Bioconductor project. To install the package, start R and enter:

install.packages("BiocManager")
BiocManager::install("decoupleR")

Alternatively, you can instead install the latest development version from GitHub with:

BiocManager::install("saezlab/decoupleR")

Citation

Badia-i-Mompel P., Vélez 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. 2021. decoupleR: Ensemble of computational methods to infer biological activities from omics data. bioRxiv. https://doi.org/10.1101/2021.11.04.467271