progeny
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see progeny.
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: 3.16
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("progeny")
):
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")
PROGENy pathway signatures | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
Version | 1.20.0 |
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) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | easier |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | progeny_1.20.0.tar.gz |
Windows Binary | progeny_1.20.0.zip (64-bit only) |
macOS Binary (x86_64) | progeny_1.20.0.tgz |
macOS Binary (arm64) | progeny_1.20.0.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 |
Old Source Packages for BioC 3.16 | Source Archive |