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Analysis of Transposable Elements

Bioconductor version: Release (3.19)

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.

Author: Beatriz Calvo-Serra [aut], Robert Castelo [aut, cre]

Maintainer: Robert Castelo <robert.castelo at>

Citation (from within R, enter citation("atena")):


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if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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An introduction to the atena package HTML R Script
Reference Manual PDF


biocViews Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License Artistic-2.0
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
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Source Package atena_1.10.0.tar.gz
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