gep2pep

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 (3.24)

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")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DimensionReduction, GO, GeneExpression, GeneSetEnrichment, Pathways, Software
Version	1.33.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	GPL-3
Depends
Imports	repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators
System Requirements
URL

Suggests	WriteXLS, testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	gep2pep_1.33.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	gep2pep_1.33.0.tgz
macOS Binary (sonoma-arm64)	gep2pep_1.33.0.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