annotate

DOI: 10.18129/B9.bioc.annotate    

Annotation for microarrays

Bioconductor version: Release (3.6)

Using R enviroments for annotation.

Author: R. Gentleman

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("annotate")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("annotate")

 

PDF R Script Annotation Overview
PDF R Script Basic GO Usage
PDF R Script HowTo: Get HTML Output
PDF R Script HowTo: use chromosomal information
PDF R Script HOWTO: Use the online query tools
PDF R Script Using Affymetrix Probe Level Data
PDF R Script Using Data Packages
PDF R Script Using the homology package
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, GO, Pathways, Software
Version 1.56.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 13 years)
License Artistic-2.0
Depends R (>= 2.10), AnnotationDbi(>= 1.27.5), XML
Imports Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics(>= 0.13.8), RCurl
LinkingTo
Suggests hgu95av2.db, genefilter, Biostrings(>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit
SystemRequirements
Enhances
URL
Depends On Me ChromHeatMap, GeneAnswers, geneplotter, GOSim, GRridge, GSEABase, idiogram, macat, MGFM, MineICA, MLInterfaces, Neve2006, PCpheno, phenoTest, PREDA, PREDAsampledata, RpsiXML, sampleClassifier, ScISI, SemDist
Imports Me CAFE, Category, categoryCompare, CNEr, codelink, debrowser, DOQTL, DrugVsDisease, facopy, gCMAP, gCMAPWeb, GeneAnswers, genefilter, GlobalAncova, globaltest, GOstats, lumi, methyAnalysis, methylumi, MGFR, mvGST, phenoTest, qpgraph, ReportingTools, ScISI, splicegear, systemPipeR, tigre
Suggests Me adme16cod.db, ag.db, ath1121501.db, BiocCaseStudies, BiocGenerics, biomaRt, bovine.db, canine.db, canine2.db, celegans.db, chicken.db, clariomdhumanprobeset.db, clariomdhumantranscriptcluster.db, clariomshumanhttranscriptcluster.db, clariomshumantranscriptcluster.db, clariomsmousehttranscriptcluster.db, clariomsmousetranscriptcluster.db, clariomsrathttranscriptcluster.db, clariomsrattranscriptcluster.db, drosgenome1.db, drosophila2.db, ecoli2.db, GenomicRanges, GGHumanMethCancerPanelv1.db, GlobalAncova, GSAR, GSEAlm, h10kcod.db, h20kcod.db, hcg110.db, hgfocus.db, hgu133a.db, hgu133a2.db, hgu133b.db, hgu133plus2.db, hgu219.db, hgu95a.db, hgu95av2.db, hgu95b.db, hgu95c.db, hgu95d.db, hgu95e.db, hguatlas13k.db, hgubeta7.db, hguDKFZ31.db, hgug4100a.db, hgug4101a.db, hgug4110b.db, hgug4111a.db, hgug4112a.db, hgug4845a.db, hguqiagenv3.db, hi16cod.db, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hta20probeset.db, hta20transcriptcluster.db, hthgu133a.db, hthgu133b.db, hu35ksuba.db, hu35ksubb.db, hu35ksubc.db, hu35ksubd.db, hu6800.db, huex10stprobeset.db, huex10sttranscriptcluster.db, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene11stprobeset.db, hugene11sttranscriptcluster.db, hugene20stprobeset.db, hugene20sttranscriptcluster.db, hugene21stprobeset.db, hugene21sttranscriptcluster.db, HuO22.db, hwgcod.db, IlluminaHumanMethylation27k.db, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv4.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1p1.db, illuminaMousev2.db, illuminaRatv1.db, indac.db, JazaeriMetaData.db, LAPOINTE.db, lumiHumanAll.db, lumiMouseAll.db, lumiRatAll.db, m10kcod.db, m20kcod.db, maigesPack, metagenomeSeq, mgu74a.db, mgu74av2.db, mgu74b.db, mgu74bv2.db, mgu74c.db, mgu74cv2.db, mguatlas5k.db, mgug4104a.db, mgug4120a.db, mgug4121a.db, mgug4122a.db, mi16cod.db, miRBaseVersions.db, MLP, mm24kresogen.db, MmAgilentDesign026655.db, moe430a.db, moe430b.db, moex10stprobeset.db, moex10sttranscriptcluster.db, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene11stprobeset.db, mogene11sttranscriptcluster.db, mogene20stprobeset.db, mogene20sttranscriptcluster.db, mogene21stprobeset.db, mogene21sttranscriptcluster.db, mouse4302.db, mouse430a2.db, mpedbarray.db, mta10probeset.db, mta10transcriptcluster.db, mu11ksuba.db, mu11ksubb.db, Mu15v1.db, mu19ksuba.db, mu19ksubb.db, mu19ksubc.db, Mu22v3.db, mwgcod.db, Norway981.db, nugohs1a520180.db, nugomm1a520177.db, oneChannelGUI, OperonHumanV3.db, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, PartheenMetaData.db, pcxn, pedbarrayv10.db, pedbarrayv9.db, POCRCannotation.db, porcine.db, puma, r10kcod.db, rae230a.db, rae230b.db, raex10stprobeset.db, raex10sttranscriptcluster.db, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene11stprobeset.db, ragene11sttranscriptcluster.db, ragene20stprobeset.db, ragene20sttranscriptcluster.db, ragene21stprobeset.db, ragene21sttranscriptcluster.db, rat2302.db, rgu34a.db, rgu34b.db, rgu34c.db, rguatlas4k.db, rgug4105a.db, rgug4130a.db, rgug4131a.db, ri16cod.db, RnAgilentDesign028282.db, RnBeads, rnu34.db, Roberts2005Annotation.db, rta10probeset.db, rta10transcriptcluster.db, rtu34.db, rwgcod.db, SHDZ.db, siggenes, SummarizedExperiment, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db
Build Report  

Package Archives

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

Source Package annotate_1.56.2.tar.gz
Windows Binary annotate_1.56.2.zip
Mac OS X 10.11 (El Capitan) annotate_1.56.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/annotate
Package Short Url http://bioconductor.org/packages/annotate/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: