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://comoto-pasteur-fr.github.io/DNABarcodeCompatibility/) [API documentation](https://comoto-pasteur-fr.github.io/DNABarcodeCompatibility/DNABarcodeCompatibility-manual.pdf) * Related tools: In addition, DNABarcodeCompatibility can be used from a graphical user interface. We now provide two different interfaces: 1) [Standalone Java-based graphical user interface](https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility_GUI). In such a case, additional dependencies must be installed: [Java (JDK 8 - 64 bits)](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html) and `rJava` R-package (`install.packages("rJava")`). 2) [Shiny web-based graphical user interface](https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility_Shiny). This interface can be run locally within a web browser or deployed on a web server. Support ========= Please use the [github ticket system](https://github.com/comoto-pasteur-fr/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.