DNABarcodeCompatibility

DOI: 10.18129/B9.bioc.DNABarcodeCompatibility    

This is the development version of DNABarcodeCompatibility; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.9)

The package allows one to obtain optimized 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 optimizer function to further favor the selection of barcode combinations with least redundancy of DNA barcodes.

Author: Céline Trébeau [cre] (<https://orcid.org/0000-0001-6795-5379>), Jacques Boutet de Monvel [aut] (<https://orcid.org/0000-0001-6182-3527>), Fabienne Wong Jun Tai [ctb], Raphaël Etournay [aut] (<https://orcid.org/0000-0002-2441-9274>)

Maintainer: Céline Trébeau <ctrebeau at pasteur.fr>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DNABarcodeCompatibility", version = "3.9")

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

Details

biocViews Preprocessing, Sequencing, Software
Version 0.99.9
License GPL-2
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_0.99.9.tar.gz
Windows Binary DNABarcodeCompatibility_0.99.9.zip
Mac OS X 10.11 (El Capitan) DNABarcodeCompatibility_0.99.9.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 http://bioconductor.org/packages/DNABarcodeCompatibility/
Package Downloads Report Download Stats

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