DNABarcodeCompatibility
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
Bioconductor version: Release (3.20)
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("DNABarcodeCompatibility")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| Introduction to DNABarcodeCompatibility | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Preprocessing, Sequencing, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| Linking To | Rcpp, BH |
| 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | DNABarcodeCompatibility_1.22.0.zip |
| macOS Binary (x86_64) | DNABarcodeCompatibility_1.22.0.tgz |
| macOS Binary (arm64) | DNABarcodeCompatibility_1.22.0.tgz |
| 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 |