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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AtlasRDF")
AuthorJames Malone, Simon Jupp, Maryam Soleimani
Bioconductor views DataImport DataRepresentation DifferentialExpression GeneExpression GeneSetEnrichment Microarray
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...

Functions

AtlasRDF Man page
AtlasRDF-package Man page
calculateCountsForGeneLists Man page
class:enrichmentresult Man page
class:factorbackground Man page
class:generef Man page
class:pathwayresult Man page
doFishersEnrichment Man page
doFishersEnrichmentForEnsemblIds Man page
doFishersEnrichmentForGeneNames Man page
drawHeatMapForAtlasExperiment Man page
enrichmentresult Man page
enrichmentresult-class Man page
excludeSubclasses Man page
factorbackground Man page
factorbackground-class Man page
generef Man page
generef-class Man page
getAllEnsemblGenesForExFactor Man page
getExFactorURIFromLabel Man page
getExperimentIdsForGeneURI Man page
getExperimentsByDescription Man page
getExperimentURIsForGeneId Man page
getGeneListFromPubmedid Man page
getGenesForExperimentID Man page
getGenesForExperimentURI Man page
getGenesForPathwayURI Man page
getGeneUriFromEnsemblId Man page
getGeneUriFromName Man page
getLabel Man page
getOntologyMappings Man page
getPathwayForGeneId Man page
getPathwaysFromGenesAndCondition Man page
getPathwayUriFromName Man page
getRankedPathwaysForGeneIds Man page
getSpeciesSpecificEnsemblGenesForExFactor Man page
getTaxonURI Man page
includeOnlySubclasses Man page
orderEnrichmentResults Man page
pathwayresult Man page
pathwayresult-class Man page
searchForEFOTerms Man page
transcription_pathway_enrichment Man page
vizPvalues Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.