Last data update: 2014.03.03

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CranContrib
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Results 1 - 5 of 5 found.
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Bgee-class (Package: BgeeDB) : Retrieving the Bgee database data

A Reference Class to give annotation available on Bgee for particular species and the requested data (rna_seq, affymetrix)
● Data Source: BioConductor
● Keywords:
● Alias: Bgee, Bgee-class
● 0 images

listBgeeSpecies (Package: BgeeDB) : List species with Affymetrix or RNA-seq data in the Bgee database

Returns a list of available genomes for different platforms in Bgee.
● Data Source: BioConductor
● Keywords:
● Alias: listBgeeSpecies
● 0 images

loadTopAnatData (Package: BgeeDB) : Retrieve data from Bgee to perform GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

This function loads a mapping from genes to anatomical structures based on calls of expression in anatomical structures. It also loads the structure of the anatomical ontology.
● Data Source: BioConductor
● Keywords:
● Alias: loadTopAnatData
● 0 images

makeTable (Package: BgeeDB) : Formats results of the enrichment test on anatomical structures.

This function loads the results from the topGO test and creates an output table with organ names, fold enrichment and FDR. Data are sorted by p-value and only terms below the specified FDR cutoff are included.
● Data Source: BioConductor
● Keywords:
● Alias: makeTable
● 0 images

topAnat (Package: BgeeDB) : Produces an object allowing to perform GO-like enrichment of anatomical terms using the topGO package

This function produces a topAnatObject, ready to use for gene set enrichment testing using functions from the topGO package. This object uses the Uberon ontology instead of the GO ontology.
● Data Source: BioConductor
● Keywords:
● Alias: topAnat
● 0 images