Name Mode Size
DNABarcodeCompatibility-package.R 100644 1 kb
data.R 100644 1 kb
distance_filter.R 100644 4 kb
experiment_design.R 100644 7 kb
file_loading_and_checking.R 100644 1 kb
get_all_combinations.R 100644 3 kb
get_random_combinations.R 100644 3 kb
optimize_combinations.R 100644 9 kb
utils.R 100644 34 kb
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: []( * The DNABarcodeCompatibility package is also directly usable through a Shiny web application hosted by the Institut Pasteur: []( 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.