Package: ensembldb 2.31.0
Johannes Rainer
ensembldb: Utilities to create and use Ensembl-based annotation databases
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.
Authors:
ensembldb_2.31.0.tar.gz
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ensembldb.pdf |ensembldb.html✨
ensembldb/json (API)
NEWS
| # Install 'ensembldb' in R: |
| install.packages('ensembldb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jorainer/ensembldb/issues
On BioConductor:ensembldb-2.31.0(bioc 3.21)ensembldb-2.30.0(bioc 3.20)
geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl
Last updated 20 days agofrom:9c0616161f. Checks:OK: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | WARNING | Nov 01 2024 |
| R-4.5-linux | WARNING | Nov 01 2024 |
| R-4.4-win | WARNING | Nov 01 2024 |
| R-4.4-mac | OK | Nov 01 2024 |
| R-4.3-win | WARNING | Nov 01 2024 |
| R-4.3-mac | OK | Nov 01 2024 |
Exports:activeFilteraddFiltercdsBycdsToTranscriptcolumnsconvertFilterdbconndropFilterEnsDbensDbFromAHensDbFromGffensDbFromGRangesensDbFromGtfensemblVersionEntrezidFilterExonidFilterExonrankFilterexonsexonsByexonsByOverlapsfetchTablesFromEnsemblfilterfiveUTRsByTranscriptGenebiotypeFilterGeneidFiltergenesgenomeToProteingenomeToTranscriptgetGeneRegionTrackForGvizgetGenomeFaFilegetGenomeTwoBitFilehasProteinDataintronsByTranscriptkeyskeytypeslengthOflistColumnslistEnsDbslistGenebiotypeslistProteinColumnslistTableslistTxbiotypeslistUniprotDbslistUniprotMappingTypesmakeEnsembldbPackagemakeEnsemblSQLiteFromTablesmapIdsmetadataOnlyCodingTxFilterorganismpromotersProtDomIdFilterProteinDomainIdFilterProteinDomainSourceFilterproteinsproteinToGenomeproteinToTranscriptreturnFilterColumnsreturnFilterColumns<-runEnsDbAppselectSeqendFilterseqinfoseqlevelsseqlevelsStyleseqlevelsStyle<-SeqnameFilterseqnamesSeqstartFilterSeqstrandFiltershowsupportedFilterssupportedSeqlevelsStylesthreeUTRsByTranscripttoSAFtranscriptstranscriptsBytranscriptsByOverlapstranscriptToCdstranscriptToGenometranscriptToProteinTxbiotypeFilterTxExternalNameFilterTxidFilterTxIsCanonicalFilterTxSupportLevelFilterUniprotDbFilterUniprotMappingTypeFilterupdateEnsDbuseMySQL
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelazyevallifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngProtGenericsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Generating and using Ensembl based annotation packages
Rendered fromensembldb.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2022-11-09
Started: 2018-02-28
Mapping between genome, transcript and protein coordinates
Rendered fromcoordinate-mapping.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2020-01-22
Started: 2018-02-28
Querying protein features
Rendered fromproteins.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-08-21
Started: 2018-02-28
Use cases for coordinate mapping with ensembldb
Rendered fromcoordinate-mapping-use-cases.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2022-01-31
Started: 2018-11-13
Using a MySQL server backend
Rendered fromMySQL-backend.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-08-21
Started: 2018-02-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Globally add filters to an EnsDb database | activeFilter activeFilter,EnsDb-method addFilter addFilter,EnsDb-method dropFilter dropFilter,EnsDb-method filter |
| Map positions within the CDS to coordinates relative to the start of the transcript | cdsToTranscript |
| Convert an AnnotationFilter to a SQL WHERE condition for EnsDb | convertFilter,AnnotationFilter,EnsDb-method convertFilter,AnnotationFilterList,EnsDb-method |
| Deprecated functionality | Deprecated ensembldb-deprecated EntrezidFilter ExonidFilter ExonrankFilter GenebiotypeFilter GeneidFilter SeqendFilter SeqnameFilter SeqstartFilter SeqstrandFilter TxbiotypeFilter TxidFilter |
| Connect to an EnsDb object | EnsDb |
| Basic usage of an Ensembl based annotation database | dbconn dbconn,EnsDb-method EnsDb-class ensemblVersion ensemblVersion,EnsDb-method listColumns listColumns,EnsDb-method listGenebiotypes listGenebiotypes,EnsDb-method listTables listTables,EnsDb-method listTxbiotypes listTxbiotypes,EnsDb-method metadata metadata,EnsDb-method organism organism,EnsDb-method returnFilterColumns returnFilterColumns,EnsDb-method returnFilterColumns<- returnFilterColumns<-,EnsDb-method seqinfo seqinfo,EnsDb-method seqlevels seqlevels,EnsDb-method show show,EnsDb-method updateEnsDb updateEnsDb,EnsDb-method |
| Retrieve annotation data from an Ensembl based package | cdsBy cdsBy,EnsDb-method exons exons,EnsDb-method exonsBy exonsBy,EnsDb-method exonsByOverlaps,EnsDb-method fiveUTRsByTranscript,EnsDb-method genes genes,EnsDb-method intronsByTranscript,EnsDb-method promoters promoters,EnsDb-method threeUTRsByTranscript,EnsDb-method toSAF toSAF,GRangesList-method transcripts transcripts,EnsDb-method transcriptsBy transcriptsBy,EnsDb-method transcriptsByOverlaps,EnsDb-method |
| Filters supported by ensembldb | Filter-classes OnlyCodingTxFilter OnlyCodingTxFilter-class ProtDomIdFilter ProtDomIdFilter-class ProteinDomainIdFilter ProteinDomainIdFilter-class ProteinDomainSourceFilter ProteinDomainSourceFilter-class seqlevels,GRangesFilter-method seqnames,GRangesFilter-method supportedFilters,EnsDb-method TxExternalNameFilter TxExternalNameFilter-class TxIsCanonicalFilter TxIsCanonicalFilter-class TxSupportLevelFilter TxSupportLevelFilter-class UniprotDbFilter UniprotDbFilter-class UniprotMappingTypeFilter UniprotMappingTypeFilter-class |
| Map genomic coordinates to protein coordinates | genomeToProtein |
| Map genomic coordinates to transcript coordinates | genomeToTranscript |
| Utility functions | getGeneRegionTrackForGviz getGeneRegionTrackForGviz,EnsDb-method |
| Functionality related to DNA/RNA sequences | getGenomeFaFile getGenomeFaFile,EnsDb-method getGenomeTwoBitFile getGenomeTwoBitFile,EnsDb-method |
| Determine whether protein data is available in the database | hasProteinData hasProteinData,EnsDb-method |
| Calculating lengths of features | lengthOf lengthOf,EnsDb-method lengthOf,GRangesList-method |
| List EnsDb databases in a MariaDB/MySQL server | listEnsDbs |
| Generating a Ensembl annotation package from Ensembl | ensDbFromAH ensDbFromGff ensDbFromGRanges ensDbFromGtf fetchTablesFromEnsembl makeEnsembldbPackage makeEnsemblSQLiteFromTables |
| Protein related functionality | listProteinColumns listUniprotDbs listUniprotDbs,EnsDb-method listUniprotMappingTypes listUniprotMappingTypes,EnsDb-method proteins proteins,EnsDb-method |
| Map within-protein coordinates to genomic coordinates | proteinToGenome proteinToGenome,CompressedGRangesList-method proteinToGenome,EnsDb-method proteinToGenome,Preloaded-method |
| Map protein-relative coordinates to positions within the transcript | proteinToTranscript proteinToTranscript,CompressedGRangesList-method proteinToTranscript,EnsDb-method proteinToTranscript,Preloaded-method |
| Search annotations interactively | runEnsDbApp |
| Integration into the AnnotationDbi framework | columns,EnsDb-method keys,EnsDb-method keytypes,EnsDb-method mapIds,EnsDb-method select select,EnsDb-method |
| Support for other than Ensembl seqlevel style | seqlevelsStyle seqlevelsStyle,EnsDb-method seqlevelsStyle<- seqlevelsStyle<-,EnsDb-method supportedSeqlevelsStyles supportedSeqlevelsStyles,EnsDb-method |
| Map transcript-relative coordinates to positions within the CDS | transcriptToCds |
| Map transcript-relative coordinates to genomic coordinates | transcriptToGenome |
| Map transcript-relative coordinates to amino acid residues of the encoded protein | transcriptToProtein |
| Use a MariaDB/MySQL backend | useMySQL useMySQL,EnsDb-method |
