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Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: Release (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>

Citation (from within R, enter citation("progeny")):


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

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


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 1.26.0
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
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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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Source Package progeny_1.26.0.tar.gz
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