Man pages for BED
Biological Entity Dictionary (BED)

BEDBiological Entity Dictionary (BED)
bedCallCall a function on the BED graph
bedImportFeeding BED: Imports a data.frame in the BED graph database
BEIDListCreate a BEIDList
BEIDsGet the BEIDs from an object
beidsServerShiny module for searching BEIDs
beIDsToAllScopesFind all BEID and ProbeID corresponding to a BE
cacheBedCallCached neo4j call
cacheBedResultPut a BED query result in cache
checkBedCacheCheck BED cache
checkBedConnCheck if there is a connection to a BED database
checkBeIdsCheck biological entities (BE) identifiers
cleanDubiousXRefIdentify and remove dubious cross-references
clearBedCacheClear the BED cache SQLite database
compareBedInstancesCompare 2 BED database instances
connectToBedConnect to a neo4j BED database
convBeIdListsConverts lists of BE IDs
convBeIdsConverts BE IDs
convDfBeIdsAdd BE ID conversion to a data frame
dumpEnsCoreFeeding BED: Dump table from the Ensembl core database
dumpNcbiDbFeeding BED: Dump tables from the NCBI gene DATA
dumpNcbiTaxFeeding BED: Dump tables with taxonomic information from NCBI
dumpUniprotDbFeeding BED: Dump and preprocess flat dat files fro Uniprot
exploreBeExplore BE identifiers
exploreConvPathExplore the shortest convertion path between two identifiers
filterByBEIDFilter an object to keep only a set of BEIDs
findBeFind Biological Entity
findBeidsFind Biological Entity identifiers
firstCommonUpstreamBeFirst common upstream BE
focusOnScopeFocus a BE related object on a specific identifier (BEID)...
focusOnScope.BEIDListConvert a BEIDList object in a specific identifier (BEID)...
forgetBedConnectionForget a BED connection
genBePathConstruct CQL sub-query to map 2 biological entity
geneIDsToAllScopesFind all GeneID, ObjectID, TranscriptID, PeptideID and...
genProbePathIdentify the biological entity (BE) targeted by probes and...
getAllBeIdSourcesList all the source databases of BE identifiers whatever the...
getBeIdConvTableGet a conversion table between biological entity (BE)...
getBeIdDescriptionGet description of Biological Entity identifiers
getBeIdNamesGet names of Biological Entity identifiers
getBeIdNameTableGet a table of biological entity (BE) identifiers and names
getBeIdsGet biological entities identifiers
getBeIdSymbolsGet symbols of Biological Entity identifiers
getBeIdSymbolTableGet a table of biological entity (BE) identifiers and symbols
getBeIdURLGet reference URLs for BE IDs
getDirectOriginGet the direct origin of BE identifiers
getDirectProductGet the direct product of BE identifiers
getEnsemblGeneIdsFeeding BED: Download Ensembl DB and load gene information in...
getEnsemblPeptideIdsFeeding BED: Download Ensembl DB and load peptide information...
getEnsemblTranscriptIdsFeeding BED: Download Ensembl DB and load transcript...
getGeneDescriptionGet description of genes corresponding to Biological Entity...
getHomTableGet gene homologs between 2 organisms
getNcbiGeneTransPepFeeding BED: Download NCBI gene DATA and load gene,...
getOrgNamesGet organism names from taxonomy IDs
getRelevantIdsGet relevant IDs for a formerly identified BE in a context of...
getTargetedBeIdentify the biological entity (BE) targeted by probes
getTaxIdGet taxonomy ID of an organism name
getUniprotFeeding BED: Download Uniprot information in BED
guessIdScopeGuess biological entity (BE), database source and organism of...
identicalScopesCheck if two objects have the same BEID scope
is.BEIDListCheck if the provided object is a BEIDList
largestBeSourceAutoselect source of biological entity identifiers
listBeLists all the biological entities (BE) available in the BED...
listBeIdSourcesLists all the databases taken into account in the BED...
listDBAttributesList all attributes provided by a BEDB
listOrganismsLists all the organisms available in the BED database
listPlatformsLists all the probe platforms available in the BED database
loadBEFeeding BED: Load biological entities in BED
loadBeAttributeFeeding BED: Load attributes for biological entities in BED
loadBedModelFeeding BED: Load BED data model in neo4j
loadBedOtherIndexesFeeding BED: Load additional indexes in neo4j
loadBedResultGet a BED query result from cache
loadBENamesFeeding BED: Load names associated to BEIDs
loadBESymbolsFeeding BED: Load symbols associated to BEIDs
loadBEVersionFeeding BED: Load biological entities in BED with information...
loadCodesForFeeding BED: Load correspondance between genes and objects as...
loadCorrespondsToFeeding BED: Load correspondances between BE IDs
loadHistoryFeeding BED: Load history of BEIDs
loadIsAssociatedToFeeding BED: Load BE ID associations
loadIsExpressedAsFeeding BED: Load correspondance between genes and...
loadIsHomologOfFeeding BED: Load homology between BE IDs
loadIsTranslatedInFeeding BED: Load correspondance between transcripts and...
loadLuceneIndexesFeeding BED: Create Lucene indexes in neo4j
loadNCBIEntrezGOFunctionsFeeding BED: Load in BED GO functions associated to Entrez...
loadNcbiTaxFeeding BED: Load taxonomic information from NCBI
loadOrganismsFeeding BED: Load organisms in BED
loadPlfFeeding BED: Load a probes platform
loadProbesFeeding BED: Load probes targeting BE IDs
lsBedCacheList all the BED queries in cache and the total size of the...
lsBedConnectionsList all registered BED connection
metadataGet object metadata
metadata-setSet object metadata
registerBEDBFeeding BED: Register a database of biological entities in...
scopeGet the BEID scope of an object
scopesGet the BEID scopes of an object
searchBeidSearch a BEID
searchIdSearch identifier, symbol or name information
setBedVersionFeeding BED: Set the BED version
showBedDataModelShow the data model of BED
BED documentation built on March 7, 2023, 6:54 p.m.