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This is the development version of gep2pep; for the stable release version, see gep2pep.

Creation and Analysis of Pathway Expression Profiles (PEPs)

Bioconductor version: Development (3.20)

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>

Maintainer: Francesco Napolitano <franapoli at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to gep2pep HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, DimensionReduction, GO, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.25.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Imports repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators
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Suggests WriteXLS, testthat, knitr, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package gep2pep_1.25.0.tar.gz
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macOS Binary (x86_64) gep2pep_1.25.0.tgz
macOS Binary (arm64) gep2pep_1.25.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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