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annotate (version 1.50.0)

Annotation for microarrays

Description

Using R enviroments for annotation.

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Version

Version

1.50.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in annotate (1.50.0)

A function to plot by group means against each other.

annotate-defunct

Defunct Functions in Package annotate

Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.

Annotation data for the Affymetrix HGU95A GeneChip

Obtain the titles of the PubMed abstracts.

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.

Functions to Access GO data.

Functions to add arbitrary repositories

pubMedAbst-class

Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

Create a Query String for a UniGene Identifier

buildChromLocation

A function to generate an instantiation of a chromLocation class

Get the Evidence codes for a set of GO terms.

Create a Query String for an Entrez Gene Identifier

filterGOByOntology

Filter GO terms by a specified GO ontology

Get annotation map

chromLocation-class

Class chromLocation, a class for describing genes and their chromosome mappings.

Drop GO labels for specified Evidence Codes

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

A function to convert accession values to NCBI UIDs.

A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID

Classes to represent HTML pages

Get or verify valid IDs for a package.

A function to compute the probe to PubMed id incidence matrix.

Get annotation package name from chip name

entrezGeneQuery

Create a Query String for Entrez Genes

Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.

Obtain the abstracts for a set PubMed list.

Provides statistics on the types of ids used for the ACCNUM environment of a given data package

A function to query PubMed

Queries the NCBI database to obtain the sequence for a given GenBank Accession number

Functions to build HTML pages

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

DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs

Annotation data for the Affymetrix HGU95A GeneChip

A dataset which contains the lengths (in base pairs) of the human chromosomes.

List GO Identifiers by GO Ontology

Class "homoData"

A function to open the browser to Genbank with the selected gene.

A function to map from probes to unique Entrez Gene IDs

Functions to deal with Data Packages

A function to open the browser to Pubmed with the selected gene.

An interface to grep for PubMed abstracts.

Returns a list of chromosome locations from a MAP environment

Annotation data for the Affymetrix HGU95A GeneChip

Functions to map to organism IDs used by NCBI homology.

HTML Generation for PubMed Abstracts

use web to populate MIAME instance with pubmed details

Annotation data for the Affymetrix HGU95A GeneChip

A dataset to show the human genome base pair locations per chromosome.

extract publication details and abstract from annotate::pubmed function output

Get GO terms for a specified ontology

Check for GO annotation

Convenience function for getting the organism from an object or package

A function to select used genes on a chromosome from an ExpressionSet.

Function to extract data from the GEO web site

A function to compute the probe to KEGG pathway incidence matrix.

A Function To Serialize Environment