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 |