gep2pep

DOI: 10.18129/B9.bioc.gep2pep  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gep2pep.

Creation and Analysis of Pathway Expression Profiles (PEPs)

Bioconductor version: 3.16

Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

Author: Francesco Napolitano <franapoli at gmail.com>

Maintainer: Francesco Napolitano <franapoli at gmail.com>

Installation

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

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

BiocManager::install("gep2pep")

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("gep2pep")

 

HTML	R Script	Introduction to gep2pep
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, DimensionReduction, GO, GeneExpression, GeneSetEnrichment, Pathways, Software
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	GPL-3
Depends
Imports	repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators
LinkingTo
Suggests	WriteXLS, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
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	gep2pep_1.18.0.tar.gz
Windows Binary	gep2pep_1.18.0.zip
macOS Binary (x86_64)	gep2pep_1.18.0.tgz
macOS Binary (arm64)	gep2pep_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gep2pep
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gep2pep
Bioc Package Browser	https://code.bioconductor.org/browse/gep2pep/
Package Short Url	https://bioconductor.org/packages/gep2pep/
Package Downloads Report	Download Stats