Biological Entity Dictionary (BED)
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Documentation for package ‘BED’ version 1.5.2
Help Pages
| BED | Biological Entity Dictionary (BED) |
| bedCall | Call a function on the BED graph |
| bedImport | Feeding BED: Imports a data.frame in the BED graph database |
| BEIDList | Create a BEIDList |
| BEIDs | Get the BEIDs from an object |
| beidsServer | Shiny module for searching BEIDs |
| beIDsToAllScopes | Find all BEID and ProbeID corresponding to a BE |
| beidsUI | Shiny module for searching BEIDs |
| cacheBedCall | Cached neo4j call |
| cacheBedResult | Put a BED query result in cache |
| checkBedCache | Check BED cache |
| checkBedConn | Check if there is a connection to a BED database |
| checkBeIds | Check biological entities (BE) identifiers |
| 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 |
| geneIDsToAllScopes | Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism |
| genProbePath | Identify the biological entity (BE) targeted by probes and construct the CQL sub-query to map probes to the BE |
| 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 |
| getBeIdNames | Get names of Biological Entity identifiers |
| getBeIdNameTable | Get a table of biological entity (BE) identifiers and names |
| getBeIds | Get biological entities identifiers |
| getBeIdSymbols | Get symbols of Biological Entity identifiers |
| getBeIdSymbolTable | Get a table of biological entity (BE) identifiers and symbols |
| getBeIdURL | Get reference URLs for BE IDs |
| 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 |
| guessIdOrigin | Guess biological entity (BE), database source and organism of a vector of identifiers. |
| 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 |
| 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 |
| 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 |
| 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 |