genefilter

DOI: 10.18129/B9.bioc.genefilter    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see genefilter.

genefilter: methods for filtering genes from high-throughput experiments

Bioconductor version: 3.8

Some basic functions for filtering genes.

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

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

Installation

To install this package, start R (version "3.5") 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	1.64.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14 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, ampliQueso, 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, gCMAP, GGBase, GISPA, GSRI, IHWpaper, JunctionSeq, methyAnalysis, methylumi, minfi, MLInterfaces, mogsa, pcaExplorer, PECA, phenoTest, Ringo, RNAinteractMAPK, simpleaffy, TCGAbiolinks, tilingArray, XDE, zinbwave
Suggests Me	AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet, BloodCancerMultiOmics2017, categoryCompare, ClassifyR, clusterStab, codelink, 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_1.64.0.tar.gz
Windows Binary	genefilter_1.64.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	genefilter_1.64.0.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	http://bioconductor.org/packages/genefilter/
Package Downloads Report	Download Stats