annotate v1.44.0

Annotation for microarrays

Using R enviroments for annotation.

Functions in annotate

Name Description
annotate-defunct Defunct Functions in Package annotate
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
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
getSEQ Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getSYMBOL Functions to deal with Data Packages
aqListGOIDs List GO Identifiers by GO Ontology
isValidKey Get or verify valid IDs for a package.
LL2homology DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
serializeEnv A Function To Serialize Environment
setRepository Functions to add arbitrary repositories
blastSequences Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.
hgCLengths A dataset which contains the lengths (in base pairs) of the human chromosomes.
hgByChroms A dataset to show the human genome base pair locations per chromosome.
hgu95All Annotation data for the Affymetrix HGU95A GeneChip
hgu95AProbLocs chromLocation instance hgu95AProbLocs, an example of a chromLocation object
organism Convenience function for getting the organism from an object or package
p2LL A function to map from probes to unique Entrez Gene IDs
readGEOAnn Function to extract data from the GEO web site
PWAmat A function to compute the probe to KEGG pathway incidence matrix.
compatibleVersions function to check to see if the packages represented by the names passed have the same version number
buildPubMedAbst A function to generate an instantiation of a pubMedAbst class
buildChromLocation A function to generate an instantiation of a chromLocation class
dropECode Drop GO labels for specified Evidence Codes
getEvidence Get the Evidence codes for a set of GO terms.
hasGOannote Check for GO annotation
GOmnplot A function to plot by group means against each other.
pm.abstGrep An interface to grep for PubMed abstracts.
getGOTerm Functions to Access GO data.
entrezGeneByID Create a Query String for an Entrez Gene Identifier
annPkgName Get annotation package name from chip name
entrezGeneQuery Create a Query String for Entrez Genes
hgu95Achroloc Annotation data for the Affymetrix HGU95A GeneChip
getOntology Get GO terms for a specified ontology
hgu95Achrom Annotation data for the Affymetrix HGU95A GeneChip
getPMInfo extract publication details and abstract from annotate::pubmed function output
pm.titles Obtain the titles of the PubMed abstracts.
homoData-class Class "homoData"
hgu95Asym Annotation data for the Affymetrix HGU95A GeneChip
mapOrgs Functions to map to organism IDs used by NCBI homology.
makeAnchor A Function To Generate HTML Anchors
pmAbst2HTML HTML Generation for PubMed Abstracts
pubMedAbst-class Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubmed A function to open the browser to Pubmed with the selected gene.
pm.getabst Obtain the abstracts for a set PubMed list.
UniGeneQuery Create a Query String for a UniGene Identifier
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.
chrCats Returns a list of chromosome locations from a MAP environment
chromLocation-class Class chromLocation, a class for describing genes and their chromosome mappings.
genbank A function to open the browser to Genbank with the selected gene.
getAnnMap Get annotation map
getQueryLink Functions to create hypertext links that can be placed in a table cell of a HTML file
HTMLPage-class Classes to represent HTML pages
pmid2MIAME use web to populate MIAME instance with pubmed details
htmlpage Functions to build HTML pages
PMIDAmat A function to compute the probe to PubMed id incidence matrix.
pmidQuery A function to query PubMed
probesByLL A function that does reverse the mappings between probe ids and the corresponding values
GO2heatmap Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
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Details

License Artistic-2.0
LazyLoad yes
Collate AllGenerics.R ACCNUMStats.R Amat.R AnnMaps.R chromLocation.R compatipleVersions.R findNeighbors.R getData.R getPMInfo.R getSeq4ACC.R GOhelpers.R homoData.R html.R isValidKey.R LL2homology.R pmid2MIAME.R probesByLL.R pubMedAbst.R query.R readGEOAnn.R serializeEnv.R blastSequences.R zzz.R test_annotate_package.R
biocViews Annotation, Pathways, GO
Packaged 2014-07-15 23:10:57 UTC; mcarlson

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