Man pages for AtlasRDF
Gene Expression Atlas query and gene set enrichment package.
| AtlasRDF-package | Gene Expression Atlas query and gene set enrichment package. |
| calculateCountsForGeneLists | Internal function for counting genes in a gene list against... |
| doFishersEnrichment | Perform a gene set enrichment using gene list based on gene... |
| doFishersEnrichmentForEnsemblIds | Perform a gene set enrichment using gene list based on common... |
| doFishersEnrichmentForGeneNames | Perform a gene set enrichment using gene list based on common... |
| drawHeatMapForAtlasExperiment | Produce a heatmap of differentially expressed genes vs... |
| 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... |
| getExFactorURIFromLabel | Get the EFO URI from a given label |
| getExperimentIdsForGeneURI | Get ArrayExpress experiment ID which contain a gene specified... |
| getExperimentsByDescription | Search for experiments in Atlas based on a string, e.g.... |
| getExperimentURIsForGeneId | Get experiment URIs which contain a gene specified by ENSEMBL... |
| getGeneListFromPubmedid | Get gene lists in Atlas for a given pubmed id (assuming the... |
| getGenesForExperimentID | Get all of the genes reported in an experiment, speicifed by... |
| getGenesForExperimentURI | Get all of the genes reported in an experiment, speicifed by... |
| 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... |
| getPathwayForGeneId | Get pathways associated to a gene. |
| getPathwaysFromGenesAndCondition | Get pathways connected to genes which are differentially... |
| getPathwayUriFromName | Get pathway URI given a pathway name |
| getRankedPathwaysForGeneIds | Get pathway names and URIs for given gene list, sorted into... |
| getSpeciesSpecificEnsemblGenesForExFactor | Get ENSEMBL genes which have been differentially expressed... |
| getTaxonURI | Get URI of a taxon class based on the common or taxonomic... |
| includeOnlySubclasses | Filter enrichment results to only include experimental... |
| 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... |
