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

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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.

Author
James Malone, Simon Jupp, Maryam Soleimani
Date of publication
None
Maintainer
Simon Jupp <jupp@ebi.ac.uk>
License
Apache License 2.0
Version
1.10.0

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