AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.

AuthorJames Malone, Simon Jupp, Maryam Soleimani
Date of publicationNone
MaintainerSimon Jupp <jupp@ebi.ac.uk>
LicenseApache License 2.0
Version1.10.0

View on Bioconductor

Man pages

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...

Files in this package

AtlasRDF/DESCRIPTION
AtlasRDF/NAMESPACE
AtlasRDF/R
AtlasRDF/R/AllClasses.R AtlasRDF/R/AtlasRDF.R
AtlasRDF/build
AtlasRDF/build/vignette.rds
AtlasRDF/data
AtlasRDF/data/transcription_pathway_enrichment.RData
AtlasRDF/inst
AtlasRDF/inst/doc
AtlasRDF/inst/doc/AtlasRDF_vignette.R
AtlasRDF/inst/doc/AtlasRDF_vignette.Rnw
AtlasRDF/inst/doc/AtlasRDF_vignette.pdf
AtlasRDF/man
AtlasRDF/man/AtlasRDF-package.Rd AtlasRDF/man/calculateCountsForGeneLists.Rd AtlasRDF/man/doFishersEnrichment.Rd AtlasRDF/man/doFishersEnrichmentForEnsemblIds.Rd AtlasRDF/man/doFishersEnrichmentForGeneNames.Rd AtlasRDF/man/drawHeatMapForAtlasExperiment.Rd AtlasRDF/man/enrichmentresult-class.Rd AtlasRDF/man/excludeSubclasses.Rd AtlasRDF/man/factorbackground-class.Rd AtlasRDF/man/generef-class.Rd AtlasRDF/man/getAllEnsemblGenesForExFactor.Rd AtlasRDF/man/getExFactorURIFromLabel.Rd AtlasRDF/man/getExperimentIdsForGeneURI.Rd AtlasRDF/man/getExperimentURIsForGeneId.Rd AtlasRDF/man/getExperimentsByDescription.Rd AtlasRDF/man/getGeneListFromPubmedid.Rd AtlasRDF/man/getGeneUriFromEnsemblId.Rd AtlasRDF/man/getGeneUriFromName.Rd AtlasRDF/man/getGenesForExperimentID.Rd AtlasRDF/man/getGenesForExperimentURI.Rd AtlasRDF/man/getGenesForPathwayURI.Rd AtlasRDF/man/getLabel.Rd AtlasRDF/man/getOntologyMappings.Rd AtlasRDF/man/getPathwayForGeneId.Rd AtlasRDF/man/getPathwayUriFromName.Rd AtlasRDF/man/getPathwaysFromGenesAndCondition.Rd AtlasRDF/man/getRankedPathwaysForGeneIds.Rd AtlasRDF/man/getSpeciesSpecificEnsemblGenesForExFactor.Rd AtlasRDF/man/getTaxonURI.Rd AtlasRDF/man/includeOnlySubclasses.Rd AtlasRDF/man/orderEnrichmentResults.Rd AtlasRDF/man/pathwayresult-class.Rd AtlasRDF/man/searchForEFOTerms.Rd AtlasRDF/man/transcription_pathway_enrichment.Rd AtlasRDF/man/vizPvalues.Rd
AtlasRDF/vignettes
AtlasRDF/vignettes/AtlasRDF_vignette.Rnw

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