annotate: Annotation for microarrays

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Using R enviroments for annotation.

Author
R. Gentleman
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.52.0

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...

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