genefilter

DOI: 10.18129/B9.bioc.genefilter  

genefilter: methods for filtering genes from high-throughput experiments

Bioconductor version: Release (3.17)

Some basic functions for filtering genes.

Author: Robert Gentleman [aut], Vincent J. Carey [aut], Wolfgang Huber [aut], Florian Hahne [aut], Emmanuel Taiwo [ctb] ('howtogenefinder' vignette translation from Sweave to RMarkdown / HTML.), Khadijah Amusat [ctb] (Converted genefilter vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]

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

Installation

To install this package, start R (version "4.3") 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")

 

PDF	R Script	03 - Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)
HTML	R Script	howtogenefinder.knit
HTML	R Script	Using the genefilter function to filter genes from a microarray
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, Software
Version	1.82.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License	Artistic-2.0
Depends
Imports	MatrixGenerics(>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices
LinkingTo
Suggests	class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me	cellHTS2, CNTools, GeneMeta, Hiiragi2013, maEndToEnd, rnaseqGene, SISPA, sva
Imports Me	a4Base, annmap, arrayQualityMetrics, Category, cbaf, ClassifyR, countsimQC, covRNA, DEXSeq, ENmix, FlowSorted.Blood.EPIC, GISPA, GSRI, IHWpaper, metaseqR2, methylCC, methylumi, minfi, MLInterfaces, mogsa, NBAMSeq, NxtIRFcore, pcaExplorer, PECA, phenoTest, protGear, pwrEWAS, Ringo, RNAinteractMAPK, SGCP, spatialHeatmap, SpliceWiz, tilingArray, XDE, zinbwave
Suggests Me	annotate, BioNet, BloodCancerMultiOmics2017, categoryCompare, clusterStab, codelink, cola, compcodeR, curatedBladderData, curatedCRCData, curatedOvarianData, DelayedArray, EnrichedHeatmap, factDesign, ffpe, ffpeExampleData, gageData, GenomicFiles, GOstats, GSAR, GSEAlm, GSVA, logicFS, lumi, MAQCsubset, MMUPHin, npGSEA, oligo, phyloseq, pvac, qpgraph, RforProteomics, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, simplifyEnrichment, Single.mTEC.Transcriptomes, TCGAbiolinks, topGO
Links To Me
Build Report

Package Archives

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

Source Package	genefilter_1.82.1.tar.gz
Windows Binary	genefilter_1.82.1.zip
macOS Binary (x86_64)	genefilter_1.82.1.tgz
macOS Binary (arm64)	genefilter_1.82.1.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 3.17	Source Archive