gep2pep
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gep2pep.
Creation and Analysis of Pathway Expression Profiles (PEPs)
Bioconductor version: 3.9
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("gep2pep")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, DimensionReduction, GO, GeneExpression, GeneSetEnrichment, Pathways, Software |
| Version | 1.4.0 |
| 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 | |
| URL |
See More
| 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_1.4.0.tar.gz |
| Windows Binary | gep2pep_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | gep2pep_1.4.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |