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genefilter

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see genefilter.

genefilter: methods for filtering genes from high-throughput experiments


Bioconductor version: 3.11

Some basic functions for filtering genes.

Author: R. Gentleman, V. Carey, W. Huber, F. Hahne

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

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

Installation

To install this package, start R (version "4.0") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, Software
Version 1.70.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends
Imports BiocGenerics(>= 0.31.2), 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, CNTools, FlowSorted.Blood.EPIC, GeneMeta, Hiiragi2013, maEndToEnd, rnaseqGene, simpleaffy, SISPA, sva
Imports Me affyQCReport, ALPS, annmap, arrayQualityMetrics, Category, cbaf, countsimQC, covRNA, DESeq, DESeq2, DEXSeq, eisa, ENmix, exomePeak2, gCMAP, GGBase, GISPA, GSRI, IHWpaper, JunctionSeq, methyAnalysis, methylCC, methylumi, minfi, MLInterfaces, mogsa, NBAMSeq, pcaExplorer, PECA, phenoTest, pwrEWAS, Ringo, RNAinteractMAPK, simpleaffy, 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, MMUPHin, npGSEA, oligo, phyloseq, pvac, qpgraph, RforProteomics, rheumaticConditionWOLLBOLD, rtracklayer, siggenes, Single.mTEC.Transcriptomes, SSPA, TCGAbiolinks, topGO
Links To Me
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Package Archives

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

Source Package genefilter_1.70.0.tar.gz
Windows Binary genefilter_1.70.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) genefilter_1.70.0.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 3.11 Source Archive