annotate v1.48.0

Annotation for microarrays

Using R enviroments for annotation.

Functions in annotate

Name Description
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.
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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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