# atena: analysis of transposable elements in R and Bioconductor
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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](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 install it from this GitHub repo using the [remotes](https://cran.r-project.org/package=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](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/functionalgenomics/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/functionalgenomics/atena/issues) to start discussing your suggestion or, in case of a
bugfix or a straightforward feature, directly a
[pull request](https://github.com/functionalgenomics/atena/pulls).
