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genefilter

This is the development version of genefilter; for the stable release version, see genefilter.

genefilter: methods for filtering genes from high-throughput experiments


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Microarray, Software
Version 1.85.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends
Imports MatrixGenerics(>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices
System Requirements
URL
See More
Suggests class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr
Linking To
Enhances
Depends On Me cellHTS2, CNTools, GeneMeta, Hiiragi2013, maEndToEnd, rnaseqGene, sva
Imports Me a4Base, annmap, arrayQualityMetrics, Category, cbaf, ClassifyR, countsimQC, covRNA, DEXSeq, ENmix, FlowSorted.Blood.EPIC, GSRI, IHWpaper, metaseqR2, methylCC, methylumi, minfi, MLInterfaces, mogsa, NBAMSeq, pcaExplorer, PECA, phenoTest, protGear, RNAinteractMAPK, SGCP, spatialHeatmap, SpliceWiz, tilingArray, XDE, zinbwave
Suggests Me annotate, BioNet, BloodCancerMultiOmics2017, categoryCompare, clusterStab, codelink, cola, compcodeR, curatedBladderData, curatedCRCData, curatedOvarianData, DelayedArray, EnrichedHeatmap, estrogen, factDesign, ffpe, ffpeExampleData, gageData, GenomicFiles, GOstats, GSAR, GSEAlm, GSVA, HDF5Array, logicFS, lumi, MAQCsubset, MMUPHin, npGSEA, oligo, phyloseq, pvac, qpgraph, RforProteomics, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, simplifyEnrichment, Single.mTEC.Transcriptomes, TCGAbiolinks, topGO
Links To Me
Build Report Build Report

Package Archives

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

Source Package genefilter_1.85.1.tar.gz
Windows Binary genefilter_1.85.1.zip
macOS Binary (x86_64) genefilter_1.85.1.tgz
macOS Binary (arm64) genefilter_1.85.1.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