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