annotate v1.50.0

Annotation for microarrays

Using R enviroments for annotation.

Functions in annotate

Name Description
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
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Details

License Artistic-2.0
LazyLoad yes
Collate 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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