atena

DOI: 10.18129/B9.bioc.atena    

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

Analysis of Transposable Elements

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.5.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
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_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/atena/
Package Downloads Report	Download Stats