AtlasRDF-package        Gene Expression Atlas query and gene set
                        enrichment package.
doFishersEnrichment     Perform a gene set enrichment using gene list
                        based on gene URIs.
doFishersEnrichmentForEnsemblIds
                        Perform a gene set enrichment using gene list
                        based on common ENSEMBL gene IDs.
doFishersEnrichmentForGeneNames
                        Perform a gene set enrichment using gene list
                        based on common gene names.
drawHeatMapForAtlasExperiment
                        Produce a heatmap of differentially expressed
                        genes vs conditions for an Atlas experiment.
enrichmentresult-class
                        Class '"enrichmentresult"'
excludeSubclasses       Exclude subclasses of factors from enrichment
                        results
factorbackground-class
                        Class '"factorbackground"'
generef-class           Class '"generef"'
getAllEnsemblGenesForExFactor
                        Get all ENSEMBL genes reported as
                        differentially expressed for a given
                        experimental factor.
getExFactorURIFromLabel
                        Get the EFO URI from a given label
getExperimentIdsForGeneURI
                        Get ArrayExpress experiment ID which contain a
                        gene specified by URI.
getExperimentURIsForGeneId
                        Get experiment URIs which contain a gene
                        specified by ENSEMBL ID.
getExperimentsByDescription
                        Search for experiments in Atlas based on a
                        string, e.g. liver, cancer etc.
getGeneListFromPubmedid
                        Get gene lists in Atlas for a given pubmed id
                        (assuming the data is in Atlas)
getGeneUriFromEnsemblId
                        Get gene URI from an ENSEMBL ID.
getGeneUriFromName      Get URI of a gene based on the common gene
                        name.
getGenesForExperimentID
                        Get all of the genes reported in an experiment,
                        speicifed by the Atlas experiment ID.
getGenesForExperimentURI
                        Get all of the genes reported in an experiment,
                        speicifed by the Atlas experiment URI.
getGenesForPathwayURI   Get genes associated with a signalling pathway
                        from Reactome.
getLabel                Get label of an entity based on the URI.
getOntologyMappings     Get mappings for a given ontology class URI to
                        EFO using the NCBO BioPortal
getPathwayForGeneId     Get pathways associated to a gene.
getPathwayUriFromName   Get pathway URI given a pathway name
getPathwaysFromGenesAndCondition
                        Get pathways connected to genes which are
                        differentially expressed for a user specified
                        condition.
getRankedPathwaysForGeneIds
                        Get pathway names and URIs for given gene list,
                        sorted into list with most common pathways
                        first.
getSpeciesSpecificEnsemblGenesForExFactor
                        Get ENSEMBL genes which have been
                        differentially expressed for a given condition
                        and species.
getTaxonURI             Get URI of a taxon class based on the common or
                        taxonomic name.
includeOnlySubclasses   Filter enrichment results to only include
                        experimental factors of a given parent class
                        (e.g. all cancers)
orderEnrichmentResults
                        Order the results of a gene set enrichment by
                        p-value.
pathwayresult-class     Class '"pathwayresult"'
searchForEFOTerms       Search for EFO URIs from a given label text
transcription_pathway_enrichment
                        Expression Gene Set Enrichment result for
vizPvalues              Visualize the results of an enrichment
                        filtering for a specificed p-value.
