genefilter

genefilter: methods for filtering genes from high-throughput experiments

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("genefilter")):

Installation

To install this package, start R (version "4.4") 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")

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

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Details

biocViews	Microarray, Software
Version	1.86.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License	Artistic-2.0
Depends
Imports	MatrixGenerics(>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices
System Requirements
URL

Suggests	class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr
Linking To
Enhances
Depends On Me	CNTools, GeneMeta, cellHTS2, sva, Hiiragi2013, maEndToEnd, rnaseqGene, lmQCM
Imports Me	Category, ClassifyR, DEXSeq, GSRI, MLInterfaces, NBAMSeq, PECA, SGCP, SpliceWiz, XDE, a4Base, annmap, arrayQualityMetrics, cbaf, countsimQC, covRNA, metaseqR2, methylCC, methylumi, minfi, mogsa, pcaExplorer, phenoTest, protGear, spatialHeatmap, tilingArray, zinbwave, FlowSorted.Blood.EPIC, IHWpaper, RNAinteractMAPK, CoNI, dGAselID, INCATome, MiDA, netgsa
Suggests Me	BioNet, DelayedArray, EnrichedHeatmap, GOstats, GSAR, GSEAlm, GSVA, GenomicFiles, HDF5Array, MMUPHin, TCGAbiolinks, annotate, categoryCompare, clusterStab, codelink, cola, compcodeR, factDesign, ffpe, logicFS, lumi, npGSEA, oligo, phyloseq, pvac, qpgraph, rtracklayer, siggenes, simplifyEnrichment, topGO, BloodCancerMultiOmics2017, curatedBladderData, curatedCRCData, curatedOvarianData, estrogen, ffpeExampleData, gageData, MAQCsubset, RforProteomics, rheumaticConditionWOLLBOLD, Single.mTEC.Transcriptomes, maGUI, oncoPredict, SuperLearner
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	genefilter_1.86.0.tar.gz
Windows Binary (x86_64)	genefilter_1.86.0.zip
macOS Binary (x86_64)	genefilter_1.86.0.tgz
macOS Binary (arm64)	genefilter_1.86.0.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