annotate

This is the released version of annotate; for the devel version, see annotate.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Annotation for microarrays

Bioconductor version: Release (3.23)

Using R enviroments for annotation.

Author: R. Gentleman

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

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

R. Gentleman. annotate: Annotation for microarrays. doi:10.18129/B9.bioc.annotate, R package version 1.90.0, https://bioconductor.org/packages/annotate.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("annotate")

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("annotate")

Annotation Overview	PDF	R Script
Basic GO Usage	PDF	R Script
HowTo: Get HTML Output	PDF	R Script
HOWTO: Use the online query tools	PDF	R Script
Using Affymetrix Probe Level Data	PDF	R Script
HowTo: Build and use chromosomal information	HTML	R Script
Using Bioconductor's Annotation Libraries	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GO, Pathways, Software
Version	1.90.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 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), httr
System Requirements
URL

Suggests	hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me	ChromHeatMap, geneplotter, GSEABase, idiogram, MGFM, MLInterfaces, Neve2006, phenoTest, PREDA, PREDAsampledata, sampleClassifier, SemDist
Imports Me	CAFE, Category, categoryCompare, CNEr, codelink, debrowser, DrugVsDisease, geneExpressionFromGEO, genefilter, GlobalAncova, globaltest, GOstats, lumi, methylumi, MGFR, phenoTest, qpgraph, ReportingTools, SGCP, tigre, UMI4Cats
Suggests Me	adme16cod.db, ag.db, ath1121501.db, BiocGenerics, 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, clValid, drosgenome1.db, drosophila2.db, ecoli2.db, GenomicRanges, GGHumanMethCancerPanelv1.db, 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, hmdbQuery, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hta20probeset.db, hta20transcriptcluster.db, hthgu133a.db, hthgu133b.db, hthgu133plusa.db, hthgu133plusb.db, hthgu133pluspm.db, htmg430a.db, htmg430b.db, htmg430pm.db, htrat230pm.db, htratfocus.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, limorhyde, lumiHumanAll.db, lumiMouseAll.db, lumiRatAll.db, m10kcod.db, m20kcod.db, maGUI, 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, 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.Hbacteriophora.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, Orthology.eg.db, pageRank, PartheenMetaData.db, pedbarrayv10.db, pedbarrayv9.db, PhosR, 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, SomaScan.db, SummarizedExperiment, systemPipeR, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	annotate_1.90.0.tar.gz
Windows Binary (x86_64)	annotate_1.90.0.zip
macOS Binary (big-sur-x86_64)	annotate_1.90.0.tgz
macOS Binary (sonoma-arm64)	annotate_1.90.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/annotate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/annotate
Package Short Url	https://bioconductor.org/packages/annotate/
Package Downloads Report	Download Stats