siggenes

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see siggenes.

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Bioconductor version: 3.21

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 "4.5") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ExonArray, GeneExpression, Microarray, MultipleComparison, SNP, Software

Version 1.82.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20.5 years)

License LGPL (>= 2)

Depends Biobase, multtest, splines, methods

Imports stats4, grDevices, graphics, stats, scrime (>= 1.2.5)

System Requirements

URL

Suggests affy, annotate, genefilter, KernSmooth

Linking To

Enhances

Depends On Me KCsmart

Imports Me minfi, trio, XDE, DeSousa2013, NPFD

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_1.82.0.tar.gz

Windows Binary (x86_64) siggenes_1.82.0.zip

macOS Binary (x86_64) siggenes_1.82.0.tgz

macOS Binary (arm64) siggenes_1.82.0.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