About
=================
DNABarcodeCompatibility: R-package to find optimised sets of compatible barcodes for multiplex experiments.
News
=================
* The DNABarcodeCompatibility package has been approved by Bioconductor and was added to the Bioconductor release 3.9: [https://bioconductor.org/packages/DNABarcodeCompatibility](https://bioconductor.org/packages/DNABarcodeCompatibility)
* The DNABarcodeCompatibility package is also directly usable through a Shiny web application hosted by the Institut Pasteur: [https://dnabarcodecompatibility.pasteur.fr](https://dnabarcodecompatibility.pasteur.fr)
Installation
================
* Requirements
+ Install [R](https://www.r-project.org/) if not yet installed (R >= 3.6 is required).
* Within a R console, type in the following commands:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DNABarcodeCompatibility")
```
Documentation
================
[Introduction](https://www.bioconductor.org/packages/release/bioc/vignettes/DNABarcodeCompatibility/inst/doc/introduction.html)
[API documentation](https://www.bioconductor.org/packages/release/bioc/manuals/DNABarcodeCompatibility/man/DNABarcodeCompatibility.pdf)
* Related tools:
In addition, DNABarcodeCompatibility can be used from a graphical user interface :
[Shiny web-based graphical user interface](https://gitlab.pasteur.fr/ida-public/dnabarcodecompatibility_shiny). This interface can be run locally within a web browser or deployed on a web server.
Support
=========
Please use the [gitlab ticket system](https://gitlab.pasteur.fr/ida-public/dnabarcodecompatibility/-/issues) to report issues or suggestions.
We also welcome pull requests.
Reference
==========
Trébeau C, Boutet de Monvel J, Wong Jun Tai F, Petit C, Etournay R. DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments. Bioinformatics. 2018 Dec 21. [doi: 10.1093/bioinformatics/bty1030](https://doi.org/10.1093/bioinformatics/bty1030). [Epub ahead of print] PubMed PMID: 30576403.
