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. |