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. Additionally, 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
- decoupleR’s manuscript repository
- Creation of benchmarking pipelines
- Example of Kinase and TF activity estimation
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")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