This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

progeny

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 (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("progeny")

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

Documentation

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

browseVignettes("progeny")
PROGENy pathway signatures HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License Apache License (== 2.0) | file LICENSE
Depends R (>= 3.6.0)
Imports Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2
Linking To
Suggests airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
System Requirements
Enhances
URL https://github.com/saezlab/progeny
Bug Reports https://github.com/saezlab/progeny/issues
See More
Depends On Me
Imports Me easier
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package progeny_1.23.0.tar.gz
Windows Binary progeny_1.23.0.zip
macOS Binary (x86_64) progeny_1.23.0.tgz
macOS Binary (arm64) progeny_1.23.0.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/
Package Downloads Report Download Stats