DESCRIPTION

Package: atena
Type: Package
Title: Analysis of Transposable Elements
Version: 1.13.0
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,
    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: 7.3.1
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'