DNABarcodeCompatibility

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

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

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-6795-5379 , Jacques Boutet de Monvel [aut] ORCID: 0000-0001-6182-3527 , Fabienne Wong Jun Tai [ctb], Raphaël Etournay [aut] ORCID: 0000-0002-2441-9274

Maintainer: Céline Trébeau <ctrebeau at pasteur.fr>

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

Jacques Boutet de Monvel, Raphaël Etournay. DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms. doi:10.18129/B9.bioc.DNABarcodeCompatibility, R package version 1.29.0, https://bioconductor.org/packages/DNABarcodeCompatibility.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	file LICENSE
Depends	R (>= 3.6.0)
Imports	dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH
System Requirements
URL	https://dnabarcodecompatibility.pasteur.fr/
Bug Reports	https://gitlab.pasteur.fr/ida-public/dnabarcodecompatibility/-/issues

Suggests	knitr, rmarkdown, BiocStyle, testthat
Linking To	Rcpp, BH
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DNABarcodeCompatibility_1.29.0.tar.gz
Windows Binary (x86_64)	DNABarcodeCompatibility_1.29.0.zip
macOS Binary (big-sur-x86_64)	DNABarcodeCompatibility_1.29.0.tgz
macOS Binary (sonoma-arm64)	DNABarcodeCompatibility_1.29.0.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