edge
Extraction of Differential Gene Expression
Bioconductor version: Release (3.20)
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 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("edge")):
Installation
To install this package, start R (version "4.4") 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")| edge Package | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Regression, Software, TimeCourse |
| Version | 2.38.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.1.0), Biobase |
| Imports | methods, splines, sva, 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 |
| 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 | edge_2.38.0.tar.gz |
| Windows Binary (x86_64) | edge_2.38.0.zip |
| macOS Binary (x86_64) | edge_2.38.0.tgz |
| macOS Binary (arm64) | edge_2.38.0.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 |