genefilter

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see genefilter.

genefilter: methods for filtering genes from high-throughput experiments

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("genefilter")

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("genefilter")

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	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Microarray, Software
Version	1.66.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19 years)
License	Artistic-2.0
Depends
Imports	S4Vectors(>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival
System Requirements
URL

See More

Suggests	class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr
Linking To
Enhances
Depends On Me	a4Base, cellHTS2, charm, CNTools, FlowSorted.Blood.EPIC, GeneMeta, Hiiragi2013, maEndToEnd, rnaseqGene, simpleaffy, SISPA, sva
Imports Me	affyQCReport, annmap, arrayQualityMetrics, Category, cbaf, countsimQC, covRNA, DESeq, DESeq2, DEXSeq, eisa, ENmix, gCMAP, GGBase, GISPA, GSRI, IHWpaper, JunctionSeq, methyAnalysis, methylumi, minfi, MLInterfaces, mogsa, NBAMSeq, pcaExplorer, PECA, phenoTest, Ringo, RNAinteractMAPK, simpleaffy, TCGAbiolinks, tilingArray, XDE, zinbwave
Suggests Me	AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet, BloodCancerMultiOmics2017, categoryCompare, ClassifyR, clusterStab, codelink, cola, compcodeR, curatedBladderData, curatedCRCData, curatedOvarianData, DelayedArray, EnrichedHeatmap, factDesign, ffpe, ffpeExampleData, gageData, GenoGAM, GenomicFiles, GOstats, GSAR, GSEAlm, GSVA, logicFS, lumi, MAQCsubset, MCRestimate, npGSEA, oligo, phyloseq, pvac, qpgraph, RforProteomics, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, Single.mTEC.Transcriptomes, SSPA, topGO
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	genefilter_1.66.0.tar.gz
Windows Binary	genefilter_1.66.0.zip
Mac OS X 10.11 (El Capitan)	genefilter_1.66.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genefilter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genefilter
Bioc Package Browser	https://code.bioconductor.org/browse/genefilter/
Package Short Url	https://bioconductor.org/packages/genefilter/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive