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Bioconductor - atena (development version)

atena

This is the development version of atena; for the stable release version, see atena.

Analysis of Transposable Elements

Bioconductor version: Development (3.22)

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 upf.edu>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("atena")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("atena")
Details biocViews Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics Version 1.15.1 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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 System Requirements URL https://github.com/rcastelo/atena Bug Reports https://github.com/rcastelo/atena/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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