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# atena: analysis of transposable elements in R and Bioconductor [![R-CMD-check-bioc](]( [![Support posts](]( "Support site activity on atena, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.") [![Codecov test coverage](]( This `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 []( 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: ```r BiocManager::install("atena", version = "devel") ``` Alternatively, you can install it from this GitHub repo using the [remotes]( package, as follows: ``` library(remotes) install_github("functionalgenomics/atena") ``` Provided that you have installed first all its Bioconductor dependencies; see the `DESCRIPTION` file. The vignette contains an example on how to use it. ## Questions, bug reports and issues For questions and bug reports regarding the __release__ version of **atena** please use the [Bioconductor support site]( "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](