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DNABarcodeCompatibility

This is the development version of DNABarcodeCompatibility; for the stable release version, see DNABarcodeCompatibility.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("DNABarcodeCompatibility")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Preprocessing, Sequencing, Software
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License file LICENSE
Depends R (>= 3.6.0)
Imports dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods
System Requirements
URL
Bug Reports https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DNABarcodeCompatibility_1.19.0.tar.gz
Windows Binary DNABarcodeCompatibility_1.19.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DNABarcodeCompatibility
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DNABarcodeCompatibility
Bioc Package Browser https://code.bioconductor.org/browse/DNABarcodeCompatibility/
Package Short Url https://bioconductor.org/packages/DNABarcodeCompatibility/
Package Downloads Report Download Stats