annotate

DOI: 10.18129/B9.bioc.annotate  

This is the development version of annotate; for the stable release version, see annotate.

Annotation for microarrays

Bioconductor version: Development (3.18)

Using R enviroments for annotation.

Author: R. Gentleman

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

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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		Reference Manual
Text		NEWS

Details

biocViews	Annotation, GO, Pathways, Software
Version	1.79.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18.5 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
LinkingTo
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
SystemRequirements
Enhances
URL
Depends On Me	ChromHeatMap, geneplotter, GOSim, GSEABase, idiogram, macat, MGFM, MineICA, MLInterfaces, Neve2006, phenoTest, PREDA, PREDAsampledata, sampleClassifier, SemDist
Imports Me	CAFE, Category, categoryCompare, CNEr, codelink, debrowser, DrugVsDisease, 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, 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, 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, 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.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, pcxn, 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, SummarizedExperiment, systemPipeR, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db
Links To Me
Build Report

Package Archives

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

Source Package	annotate_1.79.0.tar.gz
Windows Binary	annotate_1.79.0.zip (64-bit only)
macOS Binary (x86_64)	annotate_1.79.0.tgz
macOS Binary (arm64)	annotate_1.79.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/annotate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/annotate
Bioc Package Browser	https://code.bioconductor.org/browse/annotate/
Package Short Url	https://bioconductor.org/packages/annotate/
Package Downloads Report	Download Stats