annotate: Annotation for microarrays

Using R enviroments for annotation.

AuthorR. Gentleman
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.52.1

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...

Files in this package

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

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