{ "_id": "6a143dc1acfb0bcc41d430bc", "Package": "ensembldb", "Type": "Package", "Title": "Utilities to create and use Ensembl-based annotation databases", "Version": "2.37.1", "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\",\nemail = \"johannes.rainer@eurac.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Tim\", family = \"Triche\",\nemail = \"tim.triche@usc.edu\",\nrole = \"ctb\"),\nperson(given = \"Christian\", family = \"Weichenberger\",\nemail = \"christian.weichenberger@eurac.edu\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2176-0274\")),\nperson(given = \"Sebastian\", family = \"Gibb\",\nemail = \"mail@sebastiangibb.de\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-7406-4443\")),\nperson(given = \"Laurent\", family = \"Gatto\",\nemail = \"lg390@cam.ac.uk\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-1520-2268\")),\nperson(given = \"Boyu\", family = \"Yu\",\nemail = \"boyu.yu.tim@gmail.com\",\nrole = \"ctb\"))", "Author": "Johannes Rainer with contributions\nfrom Tim Triche, Sebastian Gibb, Laurent Gatto Christian\nWeichenberger and Boyu Yu.", "Maintainer": "Johannes Rainer ", "URL": "https://github.com/jorainer/ensembldb", "BugReports": "https://github.com/jorainer/ensembldb/issues", "VignetteBuilder": "knitr", "Description": "The package provides functions to create and use\ntranscript centric annotation databases/packages. The\nannotation for the databases are directly fetched from Ensembl\nusing their Perl API. The functionality and data is similar to\nthat of the TxDb packages from the GenomicFeatures package,\nbut, in addition to retrieve all gene/transcript models and\nannotations from the database, ensembldb provides a filter\nframework allowing to retrieve annotations for specific entries\nlike genes encoded on a chromosome region or transcript models\nof lincRNA genes. EnsDb databases built with ensembldb contain\nalso protein annotations and mappings between proteins and\ntheir encoding transcripts. Finally, ensembldb provides\nfunctions to map between genomic, transcript and protein\ncoordinates.", "Collate": "'Classes.R' 'Deprecated.R' 'Generics.R' 'Methods-Filter.R'\n'Methods.R' 'dbhelpers.R' 'functions-EnsDb.R'\n'functions-Filter.R' 'functions-create-EnsDb.R'\n'functions-utils.R' 'proteinToX.R' 'transcriptToX.R'\n'genomeToX.R' 'select-methods.R' 'seqname-utils.R' 'zzz.R'", "biocViews": "Genetics, AnnotationData, Sequencing, Coverage", "License": "LGPL", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-25 09:21:41 UTC", "RemoteUrl": "https://github.com/bioc/ensembldb", "RemoteRef": "HEAD", "RemoteSha": "159ed8be7de21619c5912cd81d784174cb016dc8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 11:56:42 UTC", "User": "root" }, "MD5sum": "7c79be52641ee3ba79a8b238845155fc", "_user": "bioc", "_type": "src", "_file": 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"johannes.rainer@eurac.edu", "login": "jorainer", "mastodon": "@jorainer@fediscience.org", "bluesky": "@jorainer.bsky.social", "linkedin": "in/jorainer", "orcid": "0000-0002-6977-7147", "description": "Computational Mass Spectrometry and Metabolomics, mostly; love R coding and Emacs; member of the Bioconductor Community Advisory Board.", "uuid": 5506112 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.15.10", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Depends" }, { "package": "GenomicFeatures", "version": ">= 1.61.4", "role": "Depends" }, { "package": "AnnotationFilter", "version": ">= 1.5.2", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "RSQLite", "version": ">= 1.1", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": 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"cdsToTranscript" ] }, { "page": "convertFilter", "title": "Convert an AnnotationFilter to a SQL WHERE condition for EnsDb", "topics": [ "convertFilter,AnnotationFilter,EnsDb-method", "convertFilter,AnnotationFilterList,EnsDb-method" ] }, { "page": "Deprecated", "title": "Deprecated functionality", "topics": [ "Deprecated", "ensembldb-deprecated", "EntrezidFilter", "ExonidFilter", "ExonrankFilter", "GenebiotypeFilter", "GeneidFilter", "SeqendFilter", "SeqnameFilter", "SeqstartFilter", "SeqstrandFilter", "TxbiotypeFilter", "TxidFilter" ] }, { "page": "EnsDb", "title": "Connect to an EnsDb object", "topics": [ "EnsDb" ] }, { "page": "EnsDb-class", "title": "Basic usage of an Ensembl based annotation database", "topics": [ "dbconn", "dbconn,EnsDb-method", "EnsDb-class", "ensemblVersion", "ensemblVersion,EnsDb-method", "genome<-,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" ] }, { "page": "EnsDb-exonsBy", "title": "Retrieve annotation data from an Ensembl based package", "topics": [ "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" ] }, { "page": "Filter-classes", "title": "Filters supported by ensembldb", "topics": [ "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" ] }, { "page": "genomeToProtein", "title": "Map genomic coordinates to protein coordinates", "concept": [ "coordinate mapping functions" ], "topics": [ "genomeToProtein" ] }, { "page": "genomeToTranscript", "title": "Map genomic coordinates to transcript coordinates", "concept": [ "coordinate mapping functions" ], "topics": [ "genomeToTranscript" ] }, { "page": "EnsDb-utils", "title": "Utility functions", "topics": [ "getGeneRegionTrackForGviz", "getGeneRegionTrackForGviz,EnsDb-method" ] }, { "page": "EnsDb-sequences", "title": "Functionality related to DNA/RNA sequences", "topics": [ "getGenomeFaFile", "getGenomeFaFile,EnsDb-method", "getGenomeTwoBitFile", "getGenomeTwoBitFile,EnsDb-method" ] }, { "page": "hasProteinData-EnsDb-method", "title": "Determine whether protein data is available in the database", "topics": [ "hasProteinData", "hasProteinData,EnsDb-method" ] }, { "page": "EnsDb-lengths", "title": "Calculating lengths of features", "topics": [ "lengthOf", "lengthOf,EnsDb-method", "lengthOf,GRangesList-method" ] }, { "page": "listEnsDbs", "title": "List EnsDb databases in a MariaDB/MySQL server", "topics": [ "listEnsDbs" ] }, { "page": "makeEnsemblDbPackage", "title": "Generating a Ensembl annotation package from Ensembl", "topics": [ "ensDbFromAH", "ensDbFromGff", "ensDbFromGRanges", "ensDbFromGtf", "fetchTablesFromEnsembl", "makeEnsembldbPackage", "makeEnsemblSQLiteFromTables" ] }, { "page": "ProteinFunctionality", "title": "Protein related functionality", "topics": [ "listProteinColumns", "listUniprotDbs", "listUniprotDbs,EnsDb-method", "listUniprotMappingTypes", "listUniprotMappingTypes,EnsDb-method", "proteins", "proteins,EnsDb-method" ] }, { "page": "proteinToGenome", "title": "Map within-protein coordinates to genomic coordinates", "concept": [ "coordinate mapping functions" ], "topics": [ "proteinToGenome", "proteinToGenome,CompressedGRangesList-method", "proteinToGenome,EnsDb-method", "proteinToGenome,Preloaded-method" ] }, { "page": "proteinToTranscript", "title": "Map protein-relative coordinates to positions within the transcript", "concept": [ "coordinate mapping functions" ], "topics": [ "proteinToTranscript", "proteinToTranscript,CompressedGRangesList-method", "proteinToTranscript,EnsDb-method", "proteinToTranscript,Preloaded-method" ] }, { "page": 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"transcriptToProtein", "title": "Map transcript-relative coordinates to amino acid residues of the encoded protein", "concept": [ "coordinate mapping functions" ], "topics": [ "transcriptToProtein" ] }, { "page": "useMySQL-EnsDb-method", "title": "Use a MariaDB/MySQL backend", "topics": [ "useMySQL", "useMySQL,EnsDb-method" ] } ], "_readme": "https://github.com/bioc/ensembldb/raw/HEAD/readme.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lazyeval", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", 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