Package: atena Type: Package Title: Analysis of Transposable Elements Version: 1.19.1 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 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' Config/roxygen2/version: 8.0.0 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: 2026-07-15 16:20:45 UTC RemoteUrl: https://github.com/bioc/atena RemoteRef: HEAD RemoteSha: afce0c7b8e5492a351128b447496e4546711057d NeedsCompilation: no Packaged: 2026-07-15 20:56:13 UTC; root Author: Beatriz Calvo-Serra [aut], Robert Castelo [aut, cre] Maintainer: Robert Castelo