genefilter

DOI: 10.18129/B9.bioc.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

Bioconductor version: 3.9

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 "3.6") and enter:

if (!requireNamespace("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 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   Reference Manual
Text   NEWS

Details

biocViews Microarray, Software
Version 1.66.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 14.5 years)
License Artistic-2.0
Depends
Imports S4Vectors(>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival
LinkingTo
Suggests class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr
SystemRequirements
Enhances
URL
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  

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
Package Short Url https://bioconductor.org/packages/genefilter/
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