atena: analysis of transposable elements in R and Bioconductor

Current Bioconductor build status

• release
• development

The atena package provides access from R/Bioconductor to the following methods for the quantification of transposable element (TE) expression:

• Jin Y et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593-3599. DOI: 10.1093/bioinformatics/btv422.

• Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS. 2018;115(50):12565-12572. DOI: 10.1073/pnas.1814589115.

• Bendall et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Comp. Biol. 2019;15(9):e1006453. DOI: 10.1371/journal.pcbi.1006453.

Installation

atena has been submitted to Bioconductor.

To install the release version of this package please go to its package release landing page at https://bioconductor.org/packages/atena and follow the instructions there to install it.

This github repository contains the development version of the R/Bioconductor package atena. This version is unstable and should be used only to test new features. To install the development version you first need to install the development version of Bioconductor and then type the following line from the R shell:

BiocManager::install("atena", version="devel")

Alternatively, you can directly install it from this GitHub repo as follows:

BiocManager::install("rcastelo/atena")

Questions, bug reports and issues

For questions and bug reports regarding the release version of atena please use the Bioconductor support site. For bug reports and issues regarding this development version of atena please use the GitHub issues tab at the top-left of this page.

Contributing

Contributions to the software codebase of atena are welcome as long as contributors abide to the terms of the Bioconductor Contributor Code of Conduct. If you want to contribute to the development of GenomicScores please open an issue to start discussing your suggestion or, in case of a bugfix or a straightforward feature, directly a pull request.