siggenes

DOI: 10.18129/B9.bioc.siggenes  

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Bioconductor version: Release (3.16)

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>

Installation

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

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

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")

 

HTML		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
PDF	R Script	siggenes Manual
PDF		siggenesRnews.pdf
HTML		summary.ebam.html
HTML		summary.sam.html
PDF		Reference Manual

Details

biocViews	DifferentialExpression, ExonArray, GeneExpression, Microarray, MultipleComparison, SNP, Software
Version	1.72.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	LGPL (>= 2)
Depends	Biobase, multtest, splines, methods
Imports	stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
LinkingTo
Suggests	affy, annotate, genefilter, KernSmooth
SystemRequirements
Enhances
URL
Depends On Me	KCsmart
Imports Me	coexnet, DeSousa2013, minfi, trio, XDE
Suggests Me	GCSscore, logicFS
Links To Me
Build Report

Package Archives

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

Source Package	siggenes_1.72.0.tar.gz
Windows Binary	siggenes_1.72.0.zip
macOS Binary (x86_64)	siggenes_1.72.0.tgz
macOS Binary (arm64)	siggenes_1.72.0.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