DOI: 10.18129/B9.bioc.atena  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see atena.

Analysis of Transposable Elements

Bioconductor version: 3.16

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, cre], Robert Castelo [aut]

Maintainer: Beatriz Calvo-Serra <beatriz.calvo at>

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biocViews Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.4.1
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License Artistic-2.0
Depends R (>= 4.1), SummarizedExperiment
Imports methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, scales, matrixStats
Suggests covr, BiocStyle, knitr, rmarkdown, RUnit
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