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atena

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

Analysis of Transposable Elements


Bioconductor version: Development (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, cre], Robert Castelo [aut]

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

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

Installation

To install this package, start R (version "4.4") 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")
An introduction to the atena package HTML R Script
Reference Manual PDF

Details

biocViews Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.9.2
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, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats
System Requirements
URL https://github.com/functionalgenomics/atena
Bug Reports https://github.com/functionalgenomics/atena/issues
See More
Suggests covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer
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Package Archives

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

Source Package atena_1.9.2.tar.gz
Windows Binary
macOS Binary (x86_64) atena_1.9.2.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/atena
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/atena
Bioc Package Browser https://code.bioconductor.org/browse/atena/
Package Short Url https://bioconductor.org/packages/atena/
Package Downloads Report Download Stats