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annotate (version 1.48.0)
Annotation for microarrays
Description
Using R enviroments for annotation.
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Version
1.50.0
1.48.0
1.46.1
1.44.0
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Version
1.48.0
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in annotate (1.48.0)
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annotate-defunct
Defunct Functions in Package
annotate
hasGOannote
Check for GO annotation
GOmnplot
A function to plot by group means against each other.
hgu95All
Annotation data for the Affymetrix HGU95A GeneChip
annPkgName
Get annotation package name from chip name
hgu95AProbLocs
chromLocation instance hgu95AProbLocs, an example of a chromLocation object
filterGOByOntology
Filter GO terms by a specified GO ontology
findNeighbors
A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
pmidQuery
A function to query PubMed
pubmed
A function to open the browser to Pubmed with the selected gene.
accessionToUID
A function to convert accession values to NCBI UIDs.
ACCNUMStats
Provides statistics on the types of ids used for the ACCNUM environment of a given data package
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 annotate::pubmed function output
hgu95Achrom
Annotation data for the Affymetrix HGU95A GeneChip
hgu95Achroloc
Annotation data for the Affymetrix HGU95A GeneChip
pmid2MIAME
use web to populate MIAME instance with pubmed details
PMIDAmat
A function to compute the probe to PubMed id incidence matrix.
updateSymbolsToValidKeys
Take a list of symbols and translate them into the best possible ID for a package.
usedChromGenes
A function to select used genes on a chromosome from an ExpressionSet.
buildChromLocation
A function to generate an instantiation of a chromLocation class
buildPubMedAbst
A function to generate an instantiation of a pubMedAbst class
LL2homology
DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
entrezGeneByID
Create a Query String for an Entrez Gene Identifier
entrezGeneQuery
Create a Query String for Entrez Genes
isValidKey
Get or verify valid IDs for a package.
pm.abstGrep
An interface to grep for PubMed abstracts.
hgByChroms
A dataset to show the human genome base pair locations per chromosome.
hgCLengths
A dataset which contains the lengths (in base pairs) of the human chromosomes.
hgu95Asym
Annotation data for the Affymetrix HGU95A GeneChip
homoData-class
Class "homoData"
p2LL
A function to map from probes to unique Entrez Gene IDs
organism
Convenience function for getting the organism from an object or package
chromLocation-class
Class chromLocation, a class for describing genes and their chromosome mappings.
chrCats
Returns a list of chromosome locations from a MAP environment
compatibleVersions
function to check to see if the packages represented by the names passed have the same version number
pm.getabst
Obtain the abstracts for a set PubMed list.
getQueryLink
Functions to create hypertext links that can be placed in a table cell of a HTML file
dropECode
Drop GO labels for specified Evidence Codes
readGEOAnn
Function to extract data from the GEO web site
serializeEnv
A Function To Serialize Environment
GO2heatmap
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
HTMLPage-class
Classes to represent HTML pages
htmlpage
Functions to build HTML pages
makeAnchor
A Function To Generate HTML Anchors
mapOrgs
Functions to map to organism IDs used by NCBI homology.
setRepository
Functions to add arbitrary repositories
UniGeneQuery
Create a Query String for a UniGene Identifier
blastSequences
Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.
getAnnMap
Get annotation map
genbank
A function to open the browser to Genbank with the selected gene.
aqListGOIDs
List GO Identifiers by GO Ontology
getSEQ
Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getSYMBOL
Functions to deal with Data Packages
pm.titles
Obtain the titles of the PubMed abstracts.
pmAbst2HTML
HTML Generation for PubMed Abstracts
pubMedAbst-class
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
PWAmat
A function to compute the probe to KEGG pathway incidence matrix.