atena

DOI: 10.18129/B9.bioc.atena    

Analysis of Transposable Elements

Bioconductor version: Release (3.14)

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 "4.1") and enter:

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

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")

 

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

Details

biocViews Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.0.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1), SummarizedExperiment
Imports methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats
LinkingTo
Suggests covr, BiocStyle, knitr, rmarkdown, RUnit
SystemRequirements
Enhances
URL https://github.com/functionalgenomics/atena
BugReports https://github.com/functionalgenomics/atena/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package atena_1.0.1.tar.gz
Windows Binary atena_1.0.1.zip
macOS 10.13 (High Sierra) atena_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/atena
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/atena
Package Short Url https://bioconductor.org/packages/atena/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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