Package: atena
Type: Package
Title: Analysis of Transposable Elements
Version: 1.8.0
Authors@R: c(
  person("Beatriz", "Calvo-Serra", email = "beatriz.calvo@upf.edu", role = c("aut","cre")),
  person("Robert", "Castelo", email = "robert.castelo@upf.edu", role = c("aut")))
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, BiocParallel, S4Vectors,
        IRanges, GenomicRanges, GenomicAlignments, Rsamtools,
        GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub,
        matrixStats
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/functionalgenomics/atena
BugReports: https://github.com/functionalgenomics/atena/issues
RoxygenNote: 7.2.3
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: RELEASE_3_18
git_last_commit: 634a469
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 20:19:46 UTC; biocbuild
Author: Beatriz Calvo-Serra [aut, cre],
  Robert Castelo [aut]
Maintainer: Beatriz Calvo-Serra <beatriz.calvo@upf.edu>
Built: R 4.3.2; ; 2023-12-06 23:10:54 UTC; unix
