https://github.com/saezlab/progeny
R package for Pathway RespOnsive GENe activity inference
https://github.com/saezlab/progeny
Last synced: over 1 year ago
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R package for Pathway RespOnsive GENe activity inference
- Host: GitHub
- URL: https://github.com/saezlab/progeny
- Owner: saezlab
- License: apache-2.0
- Created: 2016-09-08T14:29:06.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2023-01-30T10:01:10.000Z (over 3 years ago)
- Last Synced: 2025-03-30T10:07:02.483Z (over 1 year ago)
- Language: R
- Homepage: https://saezlab.github.io/progeny/
- Size: 47.9 MB
- Stars: 101
- Watchers: 17
- Forks: 20
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PROGENy: Pathway RespOnsive GENes for activity inference 
## Overview
PROGENy is resource that leverages a large compendium of publicly available
signaling perturbation experiments to yield a common core of pathway responsive
genes for human and mouse. These, coupled with any statistical method, can be
used to infer pathway activities from bulk or single-cell transcriptomics.
This is an R package for storing the pathway signatures. To infer pathway
activities, please check out
[decoupleR](https://doi.org/10.1093/bioadv/vbac016), available in
[R](https://saezlab.github.io/decoupleR/) or
[python](https://github.com/saezlab/decoupler-py).
## Installation
Progeny is available in
[Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/progeny.html).
In addition, one can install the development version from the Github repository:
```r
## To install the package from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("progeny")
## To install the development version from the Github repo:
devtools::install_github("saezlab/progeny")
```
## Updates
Since the original release, we have implemented some extensions in PROGENy:
1. **Extension to mouse**:
Originally PROGENy was developed for the application to human data.
In a benchmark study we showed that PROGENy is also applicable to mouse data,
as described in
[Holland et al., 2019](https://doi.org/10.1016/j.bbagrm.2019.194431).
Accordingly, we included new parameters to run mouse version of PROGENy by
transforming the human genes to their mouse orthologs.
2. **Expanding Pathway Collection**:
We expanded human and mouse PROGENy with the pathways Androgen, Estrogen and
WNT.
3. **Extension to single-cell RNA-seq data**:
We showed that PROGENy can be applied to scRNA-seq data, as described in
[Holland et al., 2020](https://doi.org/10.1186/s13059-020-1949-z)
## Citation
> Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ,
Blüthgen N, Saez-Rodriguez J. 2018. Perturbation-response genes reveal signaling
footprints in cancer gene expression. _Nature Communications_:
[10.1038/s41467-017-02391-6](https://doi.org/10.1038/s41467-017-02391-6)