README.Rmd

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# decoupleR <img src="inst/figures/logo.svg" align="right" width="120" />

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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.

<p align="center" width="100%">
    <img src="https://github.com/saezlab/decoupleR/blob/master/inst/figures/graphical_abstract.png?raw=1" align="center" width="45%">
</p>

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

- [decoupleR's vignette](https://saezlab.github.io/decoupleR/articles/decoupleR.html)
- [Python implementation](https://decoupler-py.readthedocs.io/en/latest/)
- [decoupleR's manuscript repository](https://github.com/saezlab/decoupleR_manuscript)
- [Creation of benchmarking pipelines](https://github.com/saezlab/decoupleRBench)
- [Example of Kinase and TF activity estimation](https://saezlab.github.io/kinase_tf_mini_tuto/)

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

```{r bioconductor_install, eval=FALSE}
install.packages("BiocManager")
BiocManager::install("decoupleR")
```

Alternatively, you can instead install the latest development version from [GitHub](https://github.com/) with:

```{r github_install, eval=FALSE}
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