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gep2pep

Creation and Analysis of Pathway Expression Profiles (PEPs)


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("gep2pep")):

Installation

To install this package, start R (version "4.3") 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")
Introduction to gep2pep HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, DimensionReduction, GO, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends
Imports repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators
System Requirements
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Suggests WriteXLS, testthat, knitr, rmarkdown
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Package Archives

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

Source Package gep2pep_1.22.0.tar.gz
Windows Binary gep2pep_1.22.0.zip
macOS Binary (x86_64) gep2pep_1.22.0.tgz
macOS Binary (arm64) gep2pep_1.22.0.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