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annotate (version 1.48.0)

Annotation for microarrays

Description

Using R enviroments for annotation.

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Version

Version

1.48.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in annotate (1.48.0)

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.