annotate

Annotation for microarrays

Bioconductor version: 2.8

Using R enviroments for annotation.

Author: R. Gentleman

Maintainer: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

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

Details

biocViews Annotation, Pathways, GO
Depends R (>= 2.4.0), AnnotationDbi(>= 0.1.15)
Imports Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods
Suggests Biobase, hgu95av2.db, genefilter, Biostrings(>= 2.4.4), rae230a.db, rae230aprobe, tkWidgets, XML (>= 0.92-2), GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db
System Requirements
License Artistic-2.0
URL
Depends On Me Agi4x44PreProcess, ChromHeatMap, GeneAnswers, geneplotter, GGtools, GSEABase, idiogram, macat, MLInterfaces, Neve2006, ontoTools, PCpheno, phenoTest, RpsiXML, safe, ScISI
Imports Me affycoretools, Category, ChromHeatMap, codelink, GeneAnswers, genefilter, geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, lumi, methylumi, phenoTest, qpgraph, safe, 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, geneplotter, 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, hguqiagenv3.db, hi16cod.db, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hthgu133a.db, hthgu133b.db, hu35ksuba.db, hu35ksubb.db, hu35ksubc.db, hu35ksubd.db, hu6800.db, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene11stprobeset.db, hugene11sttranscriptcluster.db, HuO22.db, hwgcod.db, illuminaHumanDASLBeadID.db, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, illuminaHumanv1.db, illuminaHumanv1BeadID.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv3BeadID.db, illuminaHumanv4.db, illuminaHumanv4BeadID.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1BeadID.db, illuminaMousev1p1.db, illuminaMousev1p1BeadID.db, illuminaMousev2.db, illuminaMousev2BeadID.db, illuminaRatv1.db, illuminaRatv1BeadID.db, indac.db, JazaeriMetaData.db, LAPOINTE.db, lumiHumanAll.db, lumiMouseAll.db, lumiRatAll.db, m10kcod.db, m20kcod.db, maigesPack, 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, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene11stprobeset.db, mogene11sttranscriptcluster.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.Xl.eg.db, PartheenMetaData.db, pedbarrayv10.db, pedbarrayv9.db, POCRCannotation.db, porcine.db, puma, r10kcod.db, rae230a.db, rae230b.db, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene11stprobeset.db, ragene11sttranscriptcluster.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, tigre, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db
Version 1.30.1
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source annotate_1.30.1.tar.gz
Windows Binary annotate_1.30.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary annotate_1.30.1.tgz
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