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| AtlasRDF-package | Gene Expression Atlas query and gene set enrichment package. |
| AtlasRDF | Gene Expression Atlas query and gene set enrichment package. |
| class:enrichmentresult | Class '"enrichmentresult"' |
| class:factorbackground | Class '"factorbackground"' |
| class:generef | Class '"generef"' |
| class:pathwayresult | Class '"pathwayresult"' |
| 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 '"enrichmentresult"' |
| enrichmentresult-class | Class '"enrichmentresult"' |
| excludeSubclasses | Exclude subclasses of factors from enrichment results |
| factorbackground | Class '"factorbackground"' |
| factorbackground-class | Class '"factorbackground"' |
| generef | Class '"generef"' |
| 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. |
| getExperimentsByDescription | Search for experiments in Atlas based on a string, e.g. liver, cancer etc. |
| getExperimentURIsForGeneId | Get experiment URIs which contain a gene specified by ENSEMBL ID. |
| getGeneListFromPubmedid | Get gene lists in Atlas for a given pubmed id (assuming the data is in Atlas) |
| 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. |
| getGeneUriFromEnsemblId | Get gene URI from an ENSEMBL ID. |
| getGeneUriFromName | Get URI of a gene based on the common gene name. |
| 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. |
| getPathwaysFromGenesAndCondition | Get pathways connected to genes which are differentially expressed for a user specified condition. |
| getPathwayUriFromName | Get pathway URI given a pathway name |
| 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 '"pathwayresult"' |
| 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. |