DNABarcodeCompatibility

DOI: 10.18129/B9.bioc.DNABarcodeCompatibility    

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

Bioconductor version: Release (3.13)

The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.

Author: Céline Trébeau [cre] , Jacques Boutet de Monvel [aut] , Fabienne Wong Jun Tai [ctb], Raphaël Etournay [aut]

Maintainer: Céline Trébeau <ctrebeau at pasteur.fr>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DNABarcodeCompatibility")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DNABarcodeCompatibility")

 

HTML	R Script	Introduction to DNABarcodeCompatibility
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	file LICENSE
Depends	R (>= 3.6.0)
Imports	dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DNABarcodeCompatibility_1.8.0.tar.gz
Windows Binary	DNABarcodeCompatibility_1.8.0.zip
macOS 10.13 (High Sierra)	DNABarcodeCompatibility_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DNABarcodeCompatibility
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DNABarcodeCompatibility
Package Short Url	https://bioconductor.org/packages/DNABarcodeCompatibility/
Package Downloads Report	Download Stats