annotate

Annotation for microarrays

Bioconductor version: Development (3.0)

Using R enviroments for annotation.

Author: R. Gentleman

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

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("annotate")

To cite this package in a publication, start R and enter:

    citation("annotate")

Documentation

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 1.43.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License Artistic-2.0
Depends R (>= 2.10), AnnotationDbi(>= 0.1.15), XML
Imports Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics(>= 0.1.13)
Suggests hgu95av2.db, genefilter, Biostrings(>= 2.25.10), rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit
System Requirements
URL
Depends On Me ChromHeatMap, geneplotter, GOSim, GSEABase, idiogram, macat, MineICA, MLInterfaces, Neve2006, PCpheno, phenoTest, PREDA, PREDAsampledata, RpsiXML, ScISI
Imports Me affycoretools, CAFE, Category, categoryCompare, codelink, DrugVsDisease, gCMAP, gCMAPWeb, GeneAnswers, genefilter, GlobalAncova, globaltest, GOstats, lumi, methyAnalysis, methylumi, phenoTest, qpgraph, ReportingTools, ScISI, splicegear, tigre
Suggests Me adme16cod.db, ag.db, ath1121501.db, BiocCaseStudies, biomaRt, bovine.db, canine.db, canine2.db, celegans.db, chicken.db, drosgenome1.db, drosophila2.db, ecoli2.db, GGHumanMethCancerPanelv1.db, GlobalAncova, globaltest, GOstats, 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, 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, IlluminaHumanMethylation450k.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, 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, 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.Sco.eg.db, org.Ss.eg.db, org.Tgondii.eg.db, org.Xl.eg.db, PartheenMetaData.db, 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, rnu34.db, Roberts2005Annotation.db, rtu34.db, rwgcod.db, SHDZ.db, siggenes, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db

Package Downloads

Package Source annotate_1.43.2.tar.gz
Windows Binary annotate_1.43.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) annotate_1.43.2.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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