genefilter

genefilter: methods for filtering genes from microarray experiments

Bioconductor version: Release (2.12)

Some basic functions for filtering genes

Author: R. Gentleman, V. Carey, W. Huber, F. Hahne

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("genefilter")

To cite this package in a publication, start R and enter:

    citation("genefilter")

PDF	R Script	Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)
PDF	R Script	Diagnostics for independent filtering
PDF	R Script	How to find genes whose expression profile is similar to that of specified genes
PDF	R Script	Using the genefilter function to filter genes from a microarray dataset
PDF		Reference Manual

biocViews	Bioinformatics, Microarray, Software
Version	1.42.0
In Bioconductor since	BioC 1.6 (R-1.11) or earlier
License	Artistic-2.0
Depends
Imports	AnnotationDbi, annotate(>= 1.13.7), Biobase(>= 1.99.10), graphics, methods, stats, survival
Suggests	Biobase(>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC, DESeq, pasilla
System Requirements
URL
Depends On Me	a4Base, Agi4x44PreProcess, cellHTS, cellHTS2, charm, CNTools, GeneMeta, MLInterfaces, simpleaffy
Imports Me	affycoretools, affyQCReport, annmap, arrayQualityMetrics, Category, DESeq, DESeq2, eisa, gCMAP, GGBase, GSRI, methyAnalysis, methylumi, phenoTest, Ringo, RNAinteractMAPK, simpleaffy, tilingArray, XDE
Suggests Me	AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet, Category, categoryCompare, clusterStab, codelink, curatedOvarianData, estrogen, factDesign, ffpe, ffpeExampleData, gageData, GOstats, GSEAlm, GSVA, logicFS, lumi, MAQCsubset, MCRestimate, oligo, oneChannelGUI, phyloseq, pvac, qpgraph, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, SSPA, topGO, VanillaICE, XDE

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