progeny
This is the development version of progeny; for the stable release version, see progeny.
All Bioconductor versions of progeny
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: 3.24 · Package version: 1.35.0
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.
Author: Michael Schubert [aut], Alberto Valdeolivas [ctb] 
, Christian H. Holland [ctb] , Igor Bulanov [ctb], Aurélien Dugourd [cre, ctb]
Maintainer: Aurélien Dugourd <aurelien.dugourd at bioquant.uni-heidelberg.de>
Citation
From within R, enter citation("progeny"):
Michael Schubert. progeny: Pathway RespOnsive GENes for activity inference from gene expression. doi:10.18129/B9.bioc.progeny, R package version 1.35.0, https://bioconductor.org/packages/progeny.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("progeny")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.35.0 |
| License | Apache License (== 2.0) | file LICENSE |
| URL | https://github.com/saezlab/progeny |
| Bug Reports | https://github.com/saezlab/progeny/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 242 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/progeny/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("progeny")| PROGENy pathway signatures | HTML |
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Windows binary (x86_64) | progeny_1.35.0.zip |
| macOS binary (arm64) | progeny_1.35.0.tgz |
| macOS binary (x86_64) | progeny_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/progeny |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/progeny |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.6.0)
Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2
Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
Reverse dependencies
Suggests Me (1): autonomics