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This is the development version of progeny; for the stable release version, see progeny.

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: Development (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

PROGENy pathway signatures HTML R Script
Reference Manual PDF


biocViews FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License Apache License (== 2.0) | file LICENSE
Depends R (>= 3.6.0)
Imports Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2
System Requirements
URL https://github.com/saezlab/progeny
Bug Reports https://github.com/saezlab/progeny/issues
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Suggests airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
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Follow Installation instructions to use this package in your R session.

Source Package progeny_1.25.0.tar.gz
Windows Binary progeny_1.25.0.zip
macOS Binary (x86_64) progeny_1.25.0.tgz
macOS Binary (arm64) progeny_1.25.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/progeny
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/progeny
Bioc Package Browser https://code.bioconductor.org/browse/progeny/
Package Short Url https://bioconductor.org/packages/progeny/
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