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edge

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

Extraction of Differential Gene Expression


Bioconductor version: Development (3.19)

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 emory.edu>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Regression, Software, TimeCourse
Version 2.35.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License MIT + file LICENSE
Depends R (>= 3.1.0), Biobase
Imports methods, splines, sva, snm, qvalue(>= 1.99.0), MASS
System Requirements
URL https://github.com/jdstorey/edge
Bug Reports https://github.com/jdstorey/edge/issues
See More
Suggests testthat, knitr, ggplot2, reshape2
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Package Archives

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

Source Package edge_2.35.0.tar.gz
Windows Binary edge_2.35.0.zip
macOS Binary (x86_64) edge_2.35.0.tgz
macOS Binary (arm64) edge_2.35.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/edge
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/edge
Bioc Package Browser https://code.bioconductor.org/browse/edge/
Package Short Url https://bioconductor.org/packages/edge/
Package Downloads Report Download Stats