progeny

DOI: 10.18129/B9.bioc.progeny    

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	PROGENy pathway signatures
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version	1.18.0
In Bioconductor since	BioC 3.6 (R-3.4) (5 years)
License	Apache License (== 2.0) | file LICENSE
Depends	R (>= 3.6.0)
Imports	Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2
LinkingTo
Suggests	airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/saezlab/progeny
BugReports	https://github.com/saezlab/progeny/issues
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_1.18.0.tar.gz
Windows Binary	progeny_1.18.0.zip
macOS Binary (x86_64)	progeny_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/progeny
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/progeny
Package Short Url	https://bioconductor.org/packages/progeny/
Package Downloads Report	Download Stats