Package: sitadela
Type: Package
Title: An R package for the easy provision of simple but complete
        tab-delimited genomic annotation from a variety of sources and
        organisms
Authors@R: c(person(given="Panagiotis", family="Moulos",
    email="moulos@fleming.gr", role=c("aut", "cre")))
Depends: R (>= 4.1.0)
Imports: Biobase, BiocGenerics, biomaRt, Biostrings, Seqinfo,
        GenomicFeatures, GenomicRanges, IRanges, methods, parallel,
        Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker,
        utils
Suggests: GenomeInfoDb, BiocStyle, BSgenome, knitr, rmarkdown, RMySQL,
        RUnit
Description: Provides an interface to build a unified database of
        genomic annotations and their coordinates (gene, transcript and
        exon levels). It is aimed to be used when simple tab-delimited
        annotations (or simple GRanges objects) are required instead of
        the more complex annotation Bioconductor packages. Also useful
        when combinatorial annotation elements are reuired, such as
        RefSeq coordinates with Ensembl biotypes. Finally, it can
        download, construct and handle annotations with versioned genes
        and transcripts (where available, e.g. RefSeq and latest
        Ensembl). This is particularly useful in precision medicine
        applications where the latter must be reported.
License: Artistic-2.0
Encoding: UTF-8
URL: https://github.com/pmoulos/sitadela
biocViews: Software, WorkflowStep, RNASeq, Transcription, Sequencing,
        Transcriptomics, BiomedicalInformatics, FunctionalGenomics,
        SystemsBiology, AlternativeSplicing, DataImport, ChIPSeq
VignetteBuilder: knitr
BugReports: https://github.com/pmoulos/sitadela/issues
Version: 1.21.0
Date: 2026-03-26
Collate: 'argcheck.R' 'fromtxdb.R' 'query-ensembl.R' 'query-ncbi.R'
        'query-refseq.R' 'query-ucsc.R' 'query-utils.R' 'reduceops.R'
        'sitadela.R' 'testfuns.R' 'zzz.R'
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:16 UTC
RemoteUrl: https://github.com/bioc/sitadela
RemoteRef: HEAD
RemoteSha: a6350685c92389f4570f3a93ac6023e9cb5f5179
NeedsCompilation: no
Packaged: 2026-07-16 05:02:47 UTC; root
Author: Panagiotis Moulos [aut, cre]
Maintainer: Panagiotis Moulos <moulos@fleming.gr>