Package: atena
Type: Package
Title: Analysis of Transposable Elements
Version: 1.17.0
Authors@R: c(
    person("Beatriz", "Calvo-Serra", email="beatriz.calvo@upf.edu",
           role=c("aut")),
    person("Robert", "Castelo", email="robert.castelo@upf.edu",
           role=c("aut", "cre")))
Description: Quantify expression of transposable elements (TEs) from RNA-seq
    data through different methods, including ERVmap, TEtranscripts and
    Telescope. A common interface is provided to use each of these methods,
    which consists of building a parameter object, calling the quantification
    function with this object and getting a SummarizedExperiment object as
    output container of the quantified expression profiles. The implementation
    allows one to quantify TEs and gene transcripts in an integrated manner.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.3.0), SummarizedExperiment
Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics,
        BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures,
        GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb,
        SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli
Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit,
        TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer
biocViews: Transcription, Transcriptomics, RNASeq, Sequencing,
        Preprocessing, Software, GeneExpression, Coverage,
        DifferentialExpression, FunctionalGenomics
VignetteBuilder: knitr
URL: https://github.com/rcastelo/atena
BugReports: https://github.com/rcastelo/atena/issues
RoxygenNote: 7.3.2
Collate: 'AllGenerics.R' 'AllClasses.R' 'ERVmap.R' 'TEtranscripts.R'
        'Telescope.R' 'annotations.R' 'atena.R' 'atenaMethod.R'
        'overlappingModes.R' 'qtex.R' 'utils.R' 'zzz.R'
git_url: https://git.bioconductor.org/packages/atena
git_branch: devel
git_last_commit: 2209be2
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-11-04
NeedsCompilation: no
Packaged: 2025-11-04 21:25:34 UTC; biocbuild
Author: Beatriz Calvo-Serra [aut],
  Robert Castelo [aut, cre]
Maintainer: Robert Castelo <robert.castelo@upf.edu>
