atena

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

Analysis of Transposable Elements

Bioconductor version: Development (3.18)

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 "4.3") 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")

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

Details

biocViews	Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.7.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.3.0), SummarizedExperiment
Imports	methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats
Linking To
Suggests	covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer
System Requirements
Enhances
URL	https://github.com/functionalgenomics/atena
Bug Reports	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_1.7.0.tar.gz
Windows Binary	atena_1.7.0.zip
macOS Binary (x86_64)	atena_1.7.0.tgz
macOS Binary (arm64)	atena_1.7.0.tgz
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