DOI: 10.18129/B9.bioc.edge    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see edge.

Extraction of Differential Gene Expression

Bioconductor version: 3.8

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>

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


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PDF R Script edge Package
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Regression, Software, TimeCourse
Version 2.14.0
In Bioconductor since BioC 3.1 (R-3.2) (4 years)
License MIT + file LICENSE
Depends R (>= 3.1.0), Biobase
Imports methods, splines, sva, snm, jackstraw, qvalue(>= 1.99.0), MASS
Suggests testthat, knitr, ggplot2, reshape2
URL https://github.com/jdstorey/edge
BugReports https://github.com/jdstorey/edge/issues
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Source Package edge_2.14.0.tar.gz
Windows Binary edge_2.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) edge_2.14.0.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 http://bioconductor.org/packages/edge/
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