GeneSelector

DOI: 10.18129/B9.bioc.GeneSelector    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GeneSelector.

Stability and Aggregation of ranked gene lists

Bioconductor version: 3.8

The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.

Author: Martin Slawski <ms at cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix at ibe.med.uni-muenchen.de>.

Maintainer: Martin Slawski <ms at cs.uni-sb.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GeneSelector")

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("GeneSelector")

 

PDF	R Script	GeneSelector.pdf
PDF		Reference Manual

Details

biocViews	DifferentialExpression, Software, StatisticalMethod
Version	2.32.0
In Bioconductor since	BioC 2.2 (R-2.7) (11 years)
License	GPL (>= 2)
Depends	R (>= 2.5.1), methods, stats, Biobase
Imports	multtest, siggenes, samr, limma
LinkingTo
Suggests	multtest, siggenes, samr, limma
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	GeneSelector_2.32.0.tar.gz
Windows Binary	GeneSelector_2.32.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	GeneSelector_2.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeneSelector
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeneSelector
Package Short Url	http://bioconductor.org/packages/GeneSelector/
Package Downloads Report	Download Stats