README.md

In DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

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

• The DNABarcodeCompatibility package is also directly usable through a Shiny web application hosted by the Institut Pasteur: https://dnabarcodecompatibility.pasteur.fr

Installation

• Requirements

  • Install R 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

API documentation

• 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. In such a case, additional dependencies must be installed: Java (JDK 8 - 64 bits) and rJava R-package (install.packages("rJava")).

2) Shiny web-based graphical user interface. This interface can be run locally within a web browser or deployed on a web server.

Support

Please use the github ticket system 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. [Epub ahead of print] PubMed PMID: 30576403.

DNABarcodeCompatibility documentation built on Nov. 8, 2020, 5:36 p.m.