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AtlasRDF (version 1.8.0)

Gene Expression Atlas query and gene set enrichment package.

Description

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.

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Version

Version

1.8.0

License

Apache License 2.0

Maintainer

James Malone

Last Published

February 15th, 2017

Functions in AtlasRDF (1.8.0)

getLabel

Get label of an entity based on the URI.
excludeSubclasses

Exclude subclasses of factors from enrichment results
factorbackground-class

Class "factorbackground"
doFishersEnrichmentForGeneNames

Perform a gene set enrichment using gene list based on common gene names.
searchForEFOTerms

Search for EFO URIs from a given label text
calculateCountsForGeneLists

Internal function for counting genes in a gene list against the background
transcription_pathway_enrichment

Expression Gene Set Enrichment result for
getExperimentIdsForGeneURI

Get ArrayExpress experiment ID which contain a gene specified by URI.
getAllEnsemblGenesForExFactor

Get all ENSEMBL genes reported as differentially expressed for a given experimental factor.
pathwayresult-class

Class "pathwayresult"
doFishersEnrichmentForEnsemblIds

Perform a gene set enrichment using gene list based on common ENSEMBL gene IDs.
generef-class

Class "generef"
getExperimentURIsForGeneId

Get experiment URIs which contain a gene specified by ENSEMBL ID.
AtlasRDF-package

Gene Expression Atlas query and gene set enrichment package.
getGenesForPathwayURI

Get genes associated with a signalling pathway from Reactome.
getOntologyMappings

Get mappings for a given ontology class URI to EFO using the NCBO BioPortal
getPathwaysFromGenesAndCondition

Get pathways connected to genes which are differentially expressed for a user specified condition.
getExperimentsByDescription

Search for experiments in Atlas based on a string, e.g. liver, cancer etc.
getRankedPathwaysForGeneIds

Get pathway names and URIs for given gene list, sorted into list with most common pathways first.
getGenesForExperimentID

Get all of the genes reported in an experiment, speicifed by the Atlas experiment ID.
getGeneUriFromEnsemblId

Get gene URI from an ENSEMBL ID.
getTaxonURI

Get URI of a taxon class based on the common or taxonomic name.
getExFactorURIFromLabel

Get the EFO URI from a given label
getSpeciesSpecificEnsemblGenesForExFactor

Get ENSEMBL genes which have been differentially expressed for a given condition and species.
enrichmentresult-class

Class "enrichmentresult"
vizPvalues

Visualize the results of an enrichment filtering for a specificed p-value.
doFishersEnrichment

Perform a gene set enrichment using gene list based on gene URIs.
drawHeatMapForAtlasExperiment

Produce a heatmap of differentially expressed genes vs conditions for an Atlas experiment.
getGeneListFromPubmedid

Get gene lists in Atlas for a given pubmed id (assuming the data is in Atlas)
getGenesForExperimentURI

Get all of the genes reported in an experiment, speicifed by the Atlas experiment URI.
getGeneUriFromName

Get URI of a gene based on the common gene name.
getPathwayForGeneId

Get pathways associated to a gene.
orderEnrichmentResults

Order the results of a gene set enrichment by p-value.
includeOnlySubclasses

Filter enrichment results to only include experimental factors of a given parent class (e.g. all cancers)
getPathwayUriFromName

Get pathway URI given a pathway name