BED                     Biological Entity Dictionary (BED)
BEIDList                Create a BEIDList
BEIDs                   Get the BEIDs from an object
beIDsToAllScopes        Find all BEID and ProbeID corresponding to a BE
bedCall                 Call a function on the BED graph
bedImport               Feeding BED: Imports a data.frame in the BED
                        graph database
beidsServer             Shiny module for searching BEIDs
cacheBedCall            Cached neo4j call
cacheBedResult          Put a BED query result in cache
checkBeIds              Check biological entities (BE) identifiers
checkBedCache           Check BED cache
checkBedConn            Check if there is a connection to a BED
                        database
cleanDubiousXRef        Identify and remove dubious cross-references
clearBedCache           Clear the BED cache SQLite database
compareBedInstances     Compare 2 BED database instances
connectToBed            Connect to a neo4j BED database
convBeIdLists           Converts lists of BE IDs
convBeIds               Converts BE IDs
convDfBeIds             Add BE ID conversion to a data frame
dumpEnsCore             Feeding BED: Dump table from the Ensembl core
                        database
dumpNcbiDb              Feeding BED: Dump tables from the NCBI gene
                        DATA
dumpNcbiTax             Feeding BED: Dump tables with taxonomic
                        information from NCBI
dumpUniprotDb           Feeding BED: Dump and preprocess flat data
                        files from Uniprot
exploreBe               Explore BE identifiers
exploreConvPath         Explore the shortest convertion path between
                        two identifiers
filterByBEID            Filter an object to keep only a set of BEIDs
findBe                  Find Biological Entity
findBeids               Find Biological Entity identifiers
firstCommonUpstreamBe   First common upstream BE
focusOnScope            Focus a BE related object on a specific
                        identifier (BEID) scope
focusOnScope.BEIDList   Convert a BEIDList object in a specific
                        identifier (BEID) scope
forgetBedConnection     Forget a BED connection
genBePath               Construct CQL sub-query to map 2 biological
                        entity
genProbePath            Identify the biological entity (BE) targeted by
                        probes and construct the CQL sub-query to map
                        probes to the BE
geneIDsToAllScopes      Find all GeneID, ObjectID, TranscriptID,
                        PeptideID and ProbeID corresponding to a Gene
                        in any organism
getAllBeIdSources       List all the source databases of BE identifiers
                        whatever the BE type
getBeIdConvTable        Get a conversion table between biological
                        entity (BE) identifiers
getBeIdDescription      Get description of Biological Entity
                        identifiers
getBeIdNameTable        Get a table of biological entity (BE)
                        identifiers and names
getBeIdNames            Get names of Biological Entity identifiers
getBeIdSymbolTable      Get a table of biological entity (BE)
                        identifiers and symbols
getBeIdSymbols          Get symbols of Biological Entity identifiers
getBeIdURL              Get reference URLs for BE IDs
getBeIds                Get biological entities identifiers
getDirectOrigin         Get the direct origin of BE identifiers
getDirectProduct        Get the direct product of BE identifiers
getEnsemblGeneIds       Feeding BED: Download Ensembl DB and load gene
                        information in BED
getEnsemblPeptideIds    Feeding BED: Download Ensembl DB and load
                        peptide information in BED
getEnsemblTranscriptIds
                        Feeding BED: Download Ensembl DB and load
                        transcript information in BED
getGeneDescription      Get description of genes corresponding to
                        Biological Entity identifiers
getHomTable             Get gene homologs between 2 organisms
getNcbiGeneTransPep     Feeding BED: Download NCBI gene DATA and load
                        gene, transcript and peptide information in BED
getOrgNames             Get organism names from taxonomy IDs
getRelevantIds          Get relevant IDs for a formerly identified BE
                        in a context of interest
getTargetedBe           Identify the biological entity (BE) targeted by
                        probes
getTaxId                Get taxonomy ID of an organism name
getUniprot              Feeding BED: Download Uniprot information in
                        BED
guessIdScope            Guess biological entity (BE), database source
                        and organism of a vector of identifiers.
identicalScopes         Check if two objects have the same BEID scope
is.BEIDList             Check if the provided object is a BEIDList
largestBeSource         Autoselect source of biological entity
                        identifiers
listBe                  Lists all the biological entities (BE)
                        available in the BED database
listBeIdSources         Lists all the databases taken into account in
                        the BED database for a biological entity (BE)
listDBAttributes        List all attributes provided by a BEDB
listOrganisms           Lists all the organisms available in the BED
                        database
listPlatforms           Lists all the probe platforms available in the
                        BED database
loadBE                  Feeding BED: Load biological entities in BED
loadBENames             Feeding BED: Load names associated to BEIDs
loadBESymbols           Feeding BED: Load symbols associated to BEIDs
loadBEVersion           Feeding BED: Load biological entities in BED
                        with information about DB version
loadBeAttribute         Feeding BED: Load attributes for biological
                        entities in BED
loadBedModel            Feeding BED: Load BED data model in neo4j
loadBedOtherIndexes     Feeding BED: Load additional indexes in neo4j
loadBedResult           Get a BED query result from cache
loadCodesFor            Feeding BED: Load correspondance between genes
                        and objects as coding events
loadCorrespondsTo       Feeding BED: Load correspondances between BE
                        IDs
loadHistory             Feeding BED: Load history of BEIDs
loadIsAssociatedTo      Feeding BED: Load BE ID associations
loadIsExpressedAs       Feeding BED: Load correspondance between genes
                        and transcripts as expression events
loadIsHomologOf         Feeding BED: Load homology between BE IDs
loadIsTranslatedIn      Feeding BED: Load correspondance between
                        transcripts and peptides as translation events
loadLuceneIndexes       Feeding BED: Create Lucene indexes in neo4j
loadNCBIEntrezGOFunctions
                        Feeding BED: Load in BED GO functions
                        associated to Entrez gene IDs from NCBI
loadNcbiTax             Feeding BED: Load taxonomic information from
                        NCBI
loadOrganisms           Feeding BED: Load organisms in BED
loadPlf                 Feeding BED: Load a probes platform
loadProbes              Feeding BED: Load probes targeting BE IDs
lsBedCache              List all the BED queries in cache and the total
                        size of the cache
lsBedConnections        List all registered BED connection
metadata                Get object metadata
metadata<-              Set object metadata
registerBEDB            Feeding BED: Register a database of biological
                        entities in BED DB
scope                   Get the BEID scope of an object
scopes                  Get the BEID scopes of an object
searchBeid              Search a BEID
searchId                Search identifier, symbol or name information
setBedVersion           Feeding BED: Set the BED version
showBedDataModel        Show the data model of BED
