progeny

DOI: 10.18129/B9.bioc.progeny    

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: Release (3.13)

This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".

Author: Michael Schubert [aut], Alberto Valdeolivas [cre, ctb] , Christian H. Holland [ctb] , Igor Bulanov [ctb], Aurélien Dugourd [ctb]

Maintainer: Alberto Valdeolivas <alvaldeolivas at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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	Applying PROGENy on single-cell RNA-seq data
HTML	R Script	PROGENy pathway signatures: Application to Bulk transcriptomics
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	Apache License (== 2.0) | file LICENSE
Depends	R (>= 3.6.0)
Imports	Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra
LinkingTo
Suggests	airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/saezlab/progeny
BugReports	https://github.com/saezlab/progeny/issues
Depends On Me
Imports Me
Suggests Me	mistyR
Links To Me
Build Report

Package Archives

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

Source Package	progeny_1.14.0.tar.gz
Windows Binary	progeny_1.14.0.zip
macOS 10.13 (High Sierra)	progeny_1.14.0.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