DNABarcodeCompatibility
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
Bioconductor version: 3.23 · Package version: 1.28.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DNABarcodeCompatibility")Details
| Maintainer | Céline Trébeau <ctrebeau@pasteur.fr> |
| Author | Céline Trébeau [cre] (ORCID: <https://orcid.org/0000-0001-6795-5379>), Jacques Boutet de Monvel [aut] (ORCID: <https://orcid.org/0000-0001-6182-3527>), Fabienne Wong Jun Tai [ctb], Raphaël Etournay [aut] (ORCID: <https://orcid.org/0000-0002-2441-9274>) |
| License | file LICENSE |
| URL | https://dnabarcodecompatibility.pasteur.fr/ |
| Bug Reports | https://gitlab.pasteur.fr/ida-public/dnabarcodecompatibility/-/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Preprocessing, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/DNABarcodeCompatibility/ |
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 1.28.0, https://bioconductor.org/packages/DNABarcodeCompatibility.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | DNABarcodeCompatibility_1.28.0.tar.gz |
| Windows binary (x86_64) | DNABarcodeCompatibility_1.28.0.zip |
| macOS binary (arm64) | DNABarcodeCompatibility_1.28.0.tgz |
| macOS binary (x86_64) | DNABarcodeCompatibility_1.28.0.tgz |