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siggenes

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

Multiple Testing using SAM and Efron's Empirical Bayes Approaches


Bioconductor version: Development (3.19)

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Author: Holger Schwender

Maintainer: Holger Schwender <holger.schw at gmx.de>

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

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("siggenes")

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("siggenes")
identify.sam.html HTML
plot.ebam.html HTML
plot.finda0.html HTML
plot.sam.html HTML
print.ebam.html HTML
print.finda0.html HTML
print.sam.html HTML
siggenes Manual PDF R Script
siggenesRnews.pdf PDF
summary.ebam.html HTML
summary.sam.html HTML
Reference Manual PDF

Details

biocViews DifferentialExpression, ExonArray, GeneExpression, Microarray, MultipleComparison, SNP, Software
Version 1.77.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License LGPL (>= 2)
Depends Biobase, multtest, splines, methods
Imports stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
System Requirements
URL
See More
Suggests affy, annotate, genefilter, KernSmooth
Linking To
Enhances
Depends On Me KCsmart
Imports Me DeSousa2013, minfi, trio, XDE
Suggests Me logicFS
Links To Me
Build Report Build Report

Package Archives

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

Source Package siggenes_1.77.0.tar.gz
Windows Binary siggenes_1.77.0.zip
macOS Binary (x86_64) siggenes_1.77.0.tgz
macOS Binary (arm64) siggenes_1.77.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/siggenes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/siggenes
Bioc Package Browser https://code.bioconductor.org/browse/siggenes/
Package Short Url https://bioconductor.org/packages/siggenes/
Package Downloads Report Download Stats