edge

DOI: 10.18129/B9.bioc.edge    

Extraction of Differential Gene Expression

Bioconductor version: Release (3.15)

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass

Maintainer: John D. Storey <jstorey at princeton.edu>, Andrew J. Bass <ajbass at princeton.edu>

Installation

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

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

BiocManager::install("edge")

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("edge")

 

PDF	R Script	edge Package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Regression, Software, TimeCourse
Version	2.28.1
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.1.0), Biobase
Imports	methods, splines, sva, snm, qvalue(>= 1.99.0), MASS
LinkingTo
Suggests	testthat, knitr, ggplot2, reshape2
SystemRequirements
Enhances
URL	https://github.com/jdstorey/edge
BugReports	https://github.com/jdstorey/edge/issues
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	edge_2.28.1.tar.gz
Windows Binary	edge_2.28.1.zip
macOS Binary (x86_64)	edge_2.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/edge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/edge
Package Short Url	https://bioconductor.org/packages/edge/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive