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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 (3.19)

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")):

Installation

To install this package, start R (version "4.4") 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 1.25.0
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
See More
Suggests airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
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Package Archives

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/
Package Downloads Report Download Stats