atena
This is the development version of atena; for the stable release version, see atena.
All Bioconductor versions of atena
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Analysis of Transposable Elements
Bioconductor version: 3.24 · Package version: 1.19.2
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"):
Beatriz Calvo-Serra, Robert Castelo. atena: Analysis of Transposable Elements. doi:10.18129/B9.bioc.atena, R package version 1.19.2, https://bioconductor.org/packages/atena.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("atena")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.19.2 |
| License | Artistic-2.0 |
| URL | https://github.com/rcastelo/atena |
| Bug Reports | https://github.com/rcastelo/atena/issues |
| Last updated | 2026-08-19 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1430 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/atena/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("atena")| An introduction to the atena package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | atena_1.19.2.tar.gz |
| Windows binary (x86_64) | atena_1.19.2.zip |
| macOS binary (arm64) | atena_1.19.2.tgz |
| macOS binary (x86_64) | atena_1.19.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/atena |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/atena |
| Package Downloads Report | Download Stats |
Dependencies
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, cigarillo
Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer