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GeneidFilter() GenebiotypeFilter() EntrezidFilter() TxidFilter() TxbiotypeFilter() ExonidFilter() ExonrankFilter() SeqnameFilter() SeqstrandFilter() SeqstartFilter() SeqendFilter()
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Deprecated functionality |
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columns(<EnsDb>) keys(<EnsDb>) keytypes(<EnsDb>) mapIds(<EnsDb>) select(<EnsDb>)
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Integration into the AnnotationDbi framework |
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dbconn(<EnsDb>) ensemblVersion(<EnsDb>) listColumns(<EnsDb>) listGenebiotypes(<EnsDb>) listTxbiotypes(<EnsDb>) listTables(<EnsDb>) metadata(<EnsDb>) organism(<EnsDb>) returnFilterColumns(<EnsDb>) returnFilterColumns(<EnsDb>) `returnFilterColumns<-`(<EnsDb>) seqinfo(<EnsDb>) seqlevels(<EnsDb>) updateEnsDb(<EnsDb>)
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Basic usage of an Ensembl based annotation database |
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exons(<EnsDb>) exonsBy(<EnsDb>) intronsByTranscript(<EnsDb>) exonsByOverlaps(<EnsDb>) transcripts(<EnsDb>) transcriptsBy(<EnsDb>) transcriptsByOverlaps(<EnsDb>) promoters(<EnsDb>) genes(<EnsDb>) cdsBy(<EnsDb>) fiveUTRsByTranscript(<EnsDb>) threeUTRsByTranscript(<EnsDb>) toSAF(<GRangesList>)
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Retrieve annotation data from an Ensembl based package |
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lengthOf(<EnsDb>)
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Calculating lengths of features |
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seqlevelsStyle(<EnsDb>) `seqlevelsStyle<-`(<EnsDb>) supportedSeqlevelsStyles(<EnsDb>)
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Support for other than Ensembl seqlevel style |
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getGenomeFaFile(<EnsDb>) getGenomeTwoBitFile(<EnsDb>)
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Functionality related to DNA/RNA sequences |
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getGeneRegionTrackForGviz(<EnsDb>)
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Utility functions |
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EnsDb()
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Connect to an EnsDb object |
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OnlyCodingTxFilter() ProtDomIdFilter() ProteinDomainIdFilter() ProteinDomainSourceFilter() UniprotDbFilter() UniprotMappingTypeFilter() TxSupportLevelFilter() TxIsCanonicalFilter() TxExternalNameFilter() seqnames(<GRangesFilter>) seqlevels(<GRangesFilter>) supportedFilters(<EnsDb>)
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Filters supported by ensembldb |
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proteins(<EnsDb>) listUniprotDbs(<EnsDb>) listUniprotMappingTypes(<EnsDb>) listProteinColumns()
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Protein related functionality |
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cdsToTranscript()
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Map positions within the CDS to coordinates relative to the start of
the transcript |
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convertFilter(<AnnotationFilter>,<EnsDb>) convertFilter(<AnnotationFilterList>,<EnsDb>)
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Convert an AnnotationFilter to a SQL WHERE condition for EnsDb |
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genomeToProtein()
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Map genomic coordinates to protein coordinates |
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genomeToTranscript()
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Map genomic coordinates to transcript coordinates |
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addFilter(<EnsDb>) dropFilter(<EnsDb>) activeFilter(<EnsDb>) filter()
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Globally add filters to an EnsDb database |
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hasProteinData(<EnsDb>)
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Determine whether protein data is available in the database |
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listEnsDbs()
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List EnsDb databases in a MariaDB/MySQL server |
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ensDbFromAH() ensDbFromGRanges() ensDbFromGff() ensDbFromGtf() fetchTablesFromEnsembl() makeEnsemblSQLiteFromTables() makeEnsembldbPackage()
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Generating a Ensembl annotation package from Ensembl |
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proteinToGenome(<EnsDb>)
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Map within-protein coordinates to genomic coordinates |
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proteinToTranscript()
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Map protein-relative coordinates to positions within the transcript |
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runEnsDbApp()
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Search annotations interactively |
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transcriptToCds()
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Map transcript-relative coordinates to positions within the CDS |
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transcriptToGenome()
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Map transcript-relative coordinates to genomic coordinates |
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transcriptToProtein()
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Map transcript-relative coordinates to amino acid residues of the
encoded protein |
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useMySQL(<EnsDb>)
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Use a MariaDB/MySQL backend |