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annotate (version 1.44.0)

Annotation for microarrays

Description

Using R enviroments for annotation.

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Version

Version

1.44.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in annotate (1.44.0)

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.