progeny

DOI: 10.18129/B9.bioc.progeny    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see progeny.

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: 3.9

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 <mschu.dev at gmail.com>

Maintainer: Michael Schubert <mschu.dev at gmail.com>

Installation

To install this package, start R (version "3.6") 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	narray Usage Examples
PDF		Reference Manual
Text		LICENSE

Details

biocViews	FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	Apache License (== 2.0) | file LICENSE
Depends	R (>= 3.4.0)
Imports	Biobase
LinkingTo
Suggests	airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl
SystemRequirements
Enhances
URL	https://github.com/saezlab/progeny
BugReports	https://github.com/saezlab/progeny/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	progeny_1.6.0.tar.gz
Windows Binary	progeny_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	progeny_1.6.0.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