genefilter

genefilter: methods for filtering genes from microarray experiments

Bioconductor version: Release (2.14)

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")

Documentation

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

Details

biocViews Microarray, Software
Version 1.46.0
In Bioconductor since BioC 1.6 (R-2.1) 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, ampliQueso, cellHTS, cellHTS2, charm, CNTools, GeneMeta, Hiiragi2013, MLInterfaces, simpleaffy
Imports Me affycoretools, affyQCReport, annmap, arrayQualityMetrics, Category, DESeq, DESeq2, DEXSeq, eisa, gCMAP, GGBase, GSRI, methyAnalysis, methylumi, minfi, PECA, phenoTest, Ringo, RNAinteractMAPK, simpleaffy, tilingArray, XDE
Suggests Me AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet, Category, categoryCompare, clusterStab, codelink, compcodeR, curatedBladderData, curatedCRCData, curatedOvarianData, estrogen, factDesign, ffpe, ffpeExampleData, gageData, GenomicFiles, GOstats, GSEAlm, GSVA, logicFS, lumi, MAQCsubset, MCRestimate, npGSEA, oligo, oneChannelGUI, phyloseq, pvac, qpgraph, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, SSPA, topGO, VanillaICE, XDE

Package Downloads

Package Source genefilter_1.46.0.tar.gz
Windows Binary genefilter_1.46.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) genefilter_1.46.0.tgz
Mac OS X 10.9 (Mavericks)
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