Package: ensembldb
Type: Package
Title: Utilities to create and use Ensembl-based annotation databases
Version: 2.34.0
Authors@R: c(person(given = "Johannes", family = "Rainer",
	   email = "johannes.rainer@eurac.edu",
	   role = c("aut", "cre"),
	   comment = c(ORCID = "0000-0002-6977-7147")),
	   person(given = "Tim", family = "Triche",
	   email = "tim.triche@usc.edu",
	   role = "ctb"),
	   person(given = "Christian", family = "Weichenberger",
	   email = "christian.weichenberger@eurac.edu",
	   role = "ctb",
	   comment = c(ORCID = "0000-0002-2176-0274")),
	   person(given = "Sebastian", family = "Gibb",
	   email = "mail@sebastiangibb.de",
	   role = "ctb",
	   comment = c(ORCID = "0000-0001-7406-4443")),
	   person(given = "Laurent", family = "Gatto",
	   email = "lg390@cam.ac.uk",
	   role = "ctb",
	   comment = c(ORCID = "0000-0002-1520-2268")),
       person(given = "Boyu", family = "Yu",
	   email = "boyu.yu.tim@gmail.com",
	   role = "ctb"))
Author: Johannes Rainer <johannes.rainer@eurac.edu> with contributions
        from Tim Triche, Sebastian Gibb, Laurent Gatto Christian
        Weichenberger and Boyu Yu.
Maintainer: Johannes Rainer <johannes.rainer@eurac.edu>
URL: https://github.com/jorainer/ensembldb
BugReports: https://github.com/jorainer/ensembldb/issues
Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb
        (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>=
        1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>=
        2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl
Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>=
        1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>=
        1.5.2)
Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
        BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
        1.20.0), rmarkdown, AnnotationHub
Enhances: RMariaDB, shiny
VignetteBuilder: knitr
Description: 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.
Collate: 'Classes.R' 'Deprecated.R' 'Generics.R' 'Methods-Filter.R'
        'Methods.R' 'dbhelpers.R' 'functions-EnsDb.R'
        'functions-Filter.R' 'functions-create-EnsDb.R'
        'functions-utils.R' 'proteinToX.R' 'transcriptToX.R'
        '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
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:24:50 UTC
RemoteUrl: https://github.com/bioc/ensembldb
RemoteRef: RELEASE_3_22
RemoteSha: a13967bb64a7188cb2e54dff9c46df32a8884a6e
NeedsCompilation: no
Packaged: 2025-11-14 07:35:31 UTC; root
Built: R 4.5.2; ; 2025-11-14 07:39:32 UTC; windows
