annotate: Annotation for microarrays

Using R enviroments for annotation.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("annotate")
AuthorR. Gentleman
Bioconductor views Annotation GO Pathways
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.54.0

View on Bioconductor

Man pages

accessionToUID: A function to convert accession values to NCBI UIDs.

ACCNUMStats: Provides statistics on the types of ids used for the ACCNUM...

annotate-defunct: Defunct Functions in Package 'annotate'

annPkgName: Get annotation package name from chip name

aqListGOIDs: List GO Identifiers by GO Ontology

blastSequences: Run a blast query to NCBI for either a string or an entrez...

buildChromLocation: A function to generate an instantiation of a chromLocation...

buildPubMedAbst: A function to generate an instantiation of a pubMedAbst class

chrCats: Returns a list of chromosome locations from a MAP environment

chromLocation-class: Class chromLocation, a class for describing genes and their...

compatibleVersions: function to check to see if the packages represented by the...

dropECode: Drop GO labels for specified Evidence Codes

entrezGeneByID: Create a Query String for an Entrez Gene Identifier

entrezGeneQuery: Create a Query String for Entrez Genes

filterGOByOntology: Filter GO terms by a specified GO ontology

findNeighbors: A function to locate neighboring genes within a defined range...

genbank: A function to open the browser to Genbank with the selected...

getAnnMap: Get annotation map

getEvidence: Get the Evidence codes for a set of GO terms.

getGOTerm: Functions to Access GO data.

getOntology: Get GO terms for a specified ontology

getPMInfo: extract publication details and abstract from...

getSeq4Acc: Queries the NCBI database to obtain the sequence for a given...

getSYMBOL: Functions to deal with Data Packages

getTDRows: Functions to create hypertext links that can be placed in a...

GO2heatmap: Compute a heatmap for the specified data, for either a GO...

GOmnplot: A function to plot by group means against each other.

hasGOannote: Check for GO annotation

hgByChroms: A dataset to show the human genome base pair locations per...

hgCLengths: A dataset which contains the lengths (in base pairs) of the...

hgu95Achroloc: Annotation data for the Affymetrix HGU95A GeneChip

hgu95Achrom: Annotation data for the Affymetrix HGU95A GeneChip

hgu95All: Annotation data for the Affymetrix HGU95A GeneChip

hgu95AProbLocs: chromLocation instance hgu95AProbLocs, an example of a...

hgu95Asym: Annotation data for the Affymetrix HGU95A GeneChip

homoData-class: Class "homoData"

htmlpage: Functions to build HTML pages

HTMLPage-class: Classes to represent HTML pages

isValidkey: Get or verify valid IDs for a package.

LL2homology: DEPRECATED Functions that find the homology data for a given...

makeAnchor: A Function To Generate HTML Anchors

mapOrgs: Functions to map to organism IDs used by NCBI homology.

organism: Convenience function for getting the organism from an object...

p2LL: A function to map from probes to unique Entrez Gene IDs

pmAbst2HTML: HTML Generation for PubMed Abstracts

pm.abstGrep: An interface to grep for PubMed abstracts.

pm.getabst: Obtain the abstracts for a set PubMed list.

pmid2MIAME: use web to populate MIAME instance with pubmed details

PMIDAmat: A function to compute the probe to PubMed id incidence...

pmidQuery: A function to query PubMed

pm.titles: Obtain the titles of the PubMed abstracts.

pubmed: A function to open the browser to Pubmed with the selected...

pubMedAbst-class: Class pubMedAbst, a class to handle PubMed abstracts, and...

PWAmat: A function to compute the probe to KEGG pathway incidence...

readGEOAnn: Function to extract data from the GEO web site

serializeEnv: A Function To Serialize Environment

setRepository: Functions to add arbitrary repositories

UniGeneQuery: Create a Query String for a UniGene Identifier

updateSymbolsToValidKeys: Take a list of symbols and translate them into the best...

usedChromGenes: A function to select used genes on a chromosome from an...

Functions

. Man page
abstText Man page
abstText,pubMedAbst-method Man page
ACC2homology Man page
accessionToUID Man page
ACCNUMStats Man page
allValidKeys Man page
annotate-defunct Man page
annPkgName Man page
aqListGOIDs Man page
articleTitle Man page
articleTitle,pubMedAbst-method Man page
authors Man page
authors,pubMedAbst-method Man page
blastSequences Man page
buildChromLocation Man page
buildPubMedAbst Man page
checkArgs Man page
chrCats Man page
chromInfo Man page
chromInfo,chromLocation-method Man page
chromLengths Man page
chromLengths,chromLocation-method Man page
chromLocation Man page
chromLocation-class Man page
chromLocs Man page
chromLocs,chromLocation-method Man page
chromNames Man page
chromNames,chromLocation-method Man page
clearRepository Man page
compatibleVersions Man page
createLLChrCats Man page
createMAPIncMat Man page
dataSource Man page
dataSource,chromLocation-method Man page
dropECode Man page
entrezGeneByID Man page
entrezGeneQuery Man page
fileName Man page
fileName,HTMLPage-method Man page
filterGOByOntology Man page
findChr4LL Man page
findNeighbors Man page
FramedHTMLPage Man page
FramedHTMLPage-class Man page
FramedHTMLPage,HTMLPage-method Man page
genbank Man page
genelocator Man page
geneSymbols Man page
geneSymbols,chromLocation-method Man page
getAnnMap Man page
getBoundary Man page
getCells Man page
getEG Man page
getEvidence Man page
getGI Man page
getGO Man page
getGOChildren Man page
getGOdesc Man page
getGOOntology Man page
getGOParents Man page
getGOTerm Man page
getGPLNames Man page
getLL Man page
getOntology Man page
getOrgNameNCode Man page
getPMID Man page
getPMInfo Man page
getQuery4Affy Man page
getQuery4EN Man page
getQuery4ENSEMBL Man page
getQuery4FB Man page
getQuery4GB Man page
getQuery4LL Man page
getQuery4OMIM Man page
getQuery4SP Man page
getQuery4TR Man page
getQuery4UG Man page
getQueryLink Man page
getRepositories Man page
getSAGEFileInfo Man page
getSAGEGPL Man page
getSEQ Man page
getSYMBOL Man page
getTDRows Man page
getUniqAnnItem Man page
getValidChr Man page
GO2heatmap Man page
GOmnplot Man page
hasGOannote Man page
hgByChroms Man page
hgCLengths Man page
HGID2homology Man page
hgu95Achroloc Man page
hgu95Achrom Man page
hgu95All Man page
hgu95AProbLocs Man page
hgu95Asym Man page
homoACC Man page
homoACC,homoData-method Man page
homoData Man page
homoData-class Man page
homoHGID Man page
homoHGID,homoData-method Man page
homoLL Man page
homoLL,homoData-method Man page
homoOrg Man page
homoOrg,homoData-method Man page
homoPS Man page
homoPS,homoData-method Man page
homoType Man page
homoType,homoData-method Man page
homoURL Man page
homoURL,homoData-method Man page
htmlpage Man page
HTMLPage Man page
HTMLPage-class Man page
HTMLPage,HTMLPage-method Man page
initialize,FramedHTMLPage-method Man page
isValidKey Man page
journal Man page
journal,pubMedAbst-method Man page
KEGG2heatmap Man page
KEGG2heatmap,character,eSet,character-method Man page
KEGG2heatmap,character,matrix,character-method Man page
KEGGmnplot Man page
KEGGmnplot,character,eSet,character-method Man page
KEGGmnplot,character,matrix,character-method Man page
LL2homology Man page
lookUp Man page
mainPage Man page
mainPage,FramedHTMLPage-method Man page
mainPage,HTMLPage-method Man page
makeAnchor Man page
mapOrgs Man page
nChrom Man page
nChrom,chromLocation-method Man page
neighborGeneFinder Man page
organism Man page
organism,character-method Man page
organism,chromLocation-method Man page
orgNameNCode Man page
p2LL Man page
pageText Man page
pageText,HTMLPage-method Man page
pageTitle Man page
pageTitle,HTMLPage-method Man page
pmAbst2HTML Man page
pm.abstGrep Man page
pm.getabst Man page
pmid Man page
pmid2MIAME Man page
PMIDAmat Man page
pmid,pubMedAbst-method Man page
pmidQuery Man page
pm.titles Man page
probesByLL Man page
probesToChrom Man page
probesToChrom,chromLocation-method Man page
pubDate Man page
pubDate,pubMedAbst-method Man page
pubmed Man page
pubMedAbst Man page
pubMedAbst-class Man page
pubMedAbst,pubMedAbst-method Man page
PWAmat Man page
readGEOAnn Man page
readIDNAcc Man page
readUrl Man page
serializeDataPkgEnvs Man page
serializeEnv Man page
setRepository Man page
show Man page
show,chromLocation-method Man page
show,FramedHTMLPage-method Man page
show,homoData-method Man page
show,HTMLPage-method Man page
show,pubMedAbst-method Man page
sidePage Man page
sidePage,FramedHTMLPage-method Man page
sidePage,HTMLPage-method Man page
toFile Man page
toFile,FramedHTMLPage-method Man page
toFile,HTMLPage-method Man page
topPage Man page
topPage,FramedHTMLPage-method Man page
topPage,HTMLPage-method Man page
UniGeneQuery Man page
updateSymbolsToValidKeys Man page
usedChromGenes Man page
weightByConfi Man page
whatACC Man page

Files

DESCRIPTION
NAMESPACE
R
R/ACCNUMStats.R R/Amat.R R/AnnMaps.R R/GOhelpers.R R/LL2homology.R R/blastSequences.R R/chromLocation.R R/compatipleVersions.R R/findNeighbors.R R/getData.R R/getPMInfo.R R/getSeq4ACC.R R/homoData.R R/html.R R/isValidKey.R R/pmid2MIAME.R R/probesByLL.R R/pubMedAbst.R R/query.R R/readGEOAnn.R R/serializeEnv.R R/test_annotate_package.R R/zzz.R
TODO
build
build/vignette.rds
data
data/hgByChroms.rda
data/hgCLengths.rda
data/hgu95AProbLocs.rda
data/hgu95Achroloc.rda
data/hgu95Achrom.rda
data/hgu95All.rda
data/hgu95Asym.rda
inst
inst/NEWS.Rd
inst/doc
inst/doc/GOusage.R
inst/doc/GOusage.Rnw
inst/doc/GOusage.pdf
inst/doc/annotate.R
inst/doc/annotate.Rnw
inst/doc/annotate.pdf
inst/doc/chromLoc.R
inst/doc/chromLoc.Rnw
inst/doc/chromLoc.pdf
inst/doc/prettyOutput.R
inst/doc/prettyOutput.Rnw
inst/doc/prettyOutput.pdf
inst/doc/query.R
inst/doc/query.Rnw
inst/doc/query.pdf
inst/doc/useDataPkgs.R
inst/doc/useDataPkgs.Rnw
inst/doc/useDataPkgs.pdf
inst/doc/useHomology.R
inst/doc/useHomology.Rnw
inst/doc/useHomology.pdf
inst/doc/useProbeInfo.R
inst/doc/useProbeInfo.Rnw
inst/doc/useProbeInfo.pdf
inst/misc
inst/misc/demowrite.html
inst/misc/pmLinkGen.Rnw
inst/misc/pmLinkGen.pdf
inst/unitTests
inst/unitTests/test_getAnnMap.R
man
man/ACCNUMStats.Rd man/GO2heatmap.Rd man/GOmnplot.Rd man/HTMLPage-class.Rd man/LL2homology.Rd man/PMIDAmat.Rd man/PWAmat.Rd man/UniGeneQuery.Rd man/accessionToUID.Rd man/annPkgName.Rd man/annotate-defunct.Rd man/aqListGOIDs.Rd man/blastSequences.Rd man/buildChromLocation.Rd man/buildPubMedAbst.Rd man/chrCats.Rd man/chromLocation-class.Rd man/compatibleVersions.Rd man/dropECode.Rd man/entrezGeneByID.Rd man/entrezGeneQuery.Rd man/filterGOByOntology.Rd man/findNeighbors.Rd man/genbank.Rd man/getAnnMap.Rd man/getEvidence.Rd man/getGOTerm.Rd man/getOntology.Rd man/getPMInfo.Rd man/getSYMBOL.Rd man/getSeq4Acc.Rd man/getTDRows.Rd man/hasGOannote.Rd man/hgByChroms.Rd man/hgCLengths.Rd man/hgu95AProbLocs.Rd man/hgu95Achroloc.Rd man/hgu95Achrom.Rd man/hgu95All.Rd man/hgu95Asym.Rd man/homoData-class.Rd man/htmlpage.Rd man/isValidkey.Rd man/makeAnchor.Rd man/mapOrgs.Rd man/organism.Rd man/p2LL.Rd man/pm.abstGrep.Rd man/pm.getabst.Rd man/pm.titles.Rd man/pmAbst2HTML.Rd man/pmid2MIAME.Rd man/pmidQuery.Rd man/pubMedAbst-class.Rd man/pubmed.Rd man/readGEOAnn.Rd man/serializeEnv.Rd man/setRepository.Rd man/updateSymbolsToValidKeys.Rd man/usedChromGenes.Rd
tests
tests/annotate_unit_tests.R
vignettes
vignettes/DPChart.eps
vignettes/DPChart.png
vignettes/GOusage.Rnw
vignettes/HOWTOigenes.ps
vignettes/OLDmake
vignettes/annotate.Rfc
vignettes/annotate.Rnw
vignettes/annotate.bib
vignettes/chromLoc.Rnw
vignettes/frames.png
vignettes/noframes.png
vignettes/prettyOutput.Rnw
vignettes/query.Rnw
vignettes/useDataPkgs.Rnw
vignettes/useHomology.Rnw
vignettes/useProbeInfo.Rnw

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