# atena: analysis of transposable elements in R and Bioconductor [](https://bioconductor.org/packages/release/bioc/html/atean.html "How long has been atena in a release of Bioconductor") [](https://bioconductor.org/packages/stats/bioc/atena/ "Ranking by number of downloads. A lower number means the package is downloaded more frequently. Determined within a package type (software, experiment, annotation, workflow) and uses the number of distinct IPs for the last 12 months.") [](https://support.bioconductor.org/t/atena/ "Support site activity on atena, last 6 months: answered posts/total posts.") [](https://github.com/rcastelo/atena/actions?query=workflow%3AR-CMD-check-bioc) [](https://app.codecov.io/github/rcastelo/atena?branch=devel) <img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/atena/atena.png" height="200"/> **Current Bioconductor build status** - `release` [](https://bioconductor.org/packages/release/bioc/html/atena.html#archives "Whether atena release is available on all platforms") [](https://bioconductor.org/packages/release/bioc/html/atena.html#since "Number of recursive dependencies needed to install package") [](https://bioconductor.org/checkResults/release/bioc-LATEST/atena "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release") [](https://bioconductor.org/checkResults/release/bioc-LATEST/atena/ "Bioconductor release build") - `development` [](https://bioconductor.org/packages/devel/bioc/html/atena.html#archives "Whether atena devel is available on all platforms") [](https://bioconductor.org/packages/devel/bioc/html/atena.html#since "Number of recursive dependencies needed to install package") [](https://bioconductor.org/checkResults/devel/bioc-LATEST/atena "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release") [](https://bioconductor.org/checkResults/devel/bioc-LATEST/atena/ "Bioconductor devel build") 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](https://doi.org/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](https://doi.org/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](https://doi.org/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](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](https://bioconductor.org/developers/how-to/useDevel) and then type the following line from the R shell: ```r 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](https://support.bioconductor.org "Bioconductor support site"). For bug reports and issues regarding this __development__ version of **atena** please use the GitHub issues [tab](https://github.com/rcastelo/atena/issues) 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](https://bioconductor.org/about/code-of-conduct). If you want to contribute to the development of GenomicScores please open an [issue](https://github.com/rcastelo/atena/issues) to start discussing your suggestion or, in case of a bugfix or a straightforward feature, directly a [pull request](https://github.com/rcastelo/atena/pulls).