

# decoupleR 

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## 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. 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. This is the R version, for its faster and memory
efficient Python implementation go
[here](https://decoupler-py.readthedocs.io/en/latest/).

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

- [decoupleR’s general
  usage](https://saezlab.github.io/decoupleR/articles/decoupleR.html)
- [Pathway activity inference in bulk
  RNA-seq](https://saezlab.github.io/decoupleR/articles/pw_bk.html)
- [Pathway activity inference from
  scRNA-seq](https://saezlab.github.io/decoupleR/articles/pw_sc.html)
- [Transcription factor activity inference in bulk
  RNA-seq](https://saezlab.github.io/decoupleR/articles/tf_bk.html)
- [Transcription factor activity inference from
  scRNA-seq](https://saezlab.github.io/decoupleR/articles/tf_sc.html)
- [Example of Kinase and TF activity
  estimation](https://saezlab.github.io/kinase_tf_mini_tuto/)
- [decoupleR’s manuscript
  repository](https://github.com/saezlab/decoupleR_manuscript)
- [Python
  implementation](https://decoupler-py.readthedocs.io/en/latest/)

# Installation

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

``` r
install.packages('BiocManager')
BiocManager::install('saezlab/decoupleR')
```

Alternatively, if you find any error, try to install the latest version from GitHub:
```r
install.packages('remotes')
remotes::install_github('saezlab/decoupleR')
```

## 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](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. <https://doi.org/10.1093/bioadv/vbac016>
