DNABarcodes: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.

AuthorTilo Buschmann <tilo.buschmann.ac@gmail.com>
Date of publicationNone
MaintainerTilo Buschmann <tilo.buschmann.ac@gmail.com>
LicenseGPL-2
Version1.4.0

View on Bioconductor

Files in this package

DNABarcodes/DESCRIPTION
DNABarcodes/NAMESPACE
DNABarcodes/NEWS
DNABarcodes/R
DNABarcodes/R/RcppExports.R DNABarcodes/R/analyse.barcodes.R DNABarcodes/R/barcode.set.distances.R DNABarcodes/R/create.dnabarcodes.R DNABarcodes/R/create.pool.R DNABarcodes/R/demultiplex.R DNABarcodes/R/distance.R DNABarcodes/R/test.code.falsification.R
DNABarcodes/build
DNABarcodes/build/vignette.rds
DNABarcodes/data
DNABarcodes/data/mutatedReads.rda
DNABarcodes/data/supplierSet.rda
DNABarcodes/inst
DNABarcodes/inst/CITATION
DNABarcodes/inst/doc
DNABarcodes/inst/doc/DNABarcodes.R
DNABarcodes/inst/doc/DNABarcodes.Rmd
DNABarcodes/inst/doc/DNABarcodes.html
DNABarcodes/man
DNABarcodes/man/DNABarcodes-package.Rd DNABarcodes/man/analyse.barcodes.Rd DNABarcodes/man/barcode.set.distances.Rd DNABarcodes/man/create.dnabarcodes.Rd DNABarcodes/man/create.pool.Rd DNABarcodes/man/demultiplex.Rd DNABarcodes/man/distance.Rd DNABarcodes/man/mutatedReads.Rd DNABarcodes/man/supplierSet.Rd
DNABarcodes/src
DNABarcodes/src/DNABarcodes_init.c
DNABarcodes/src/Makevars
DNABarcodes/src/RcppExports.cpp
DNABarcodes/src/analyse_barcodes.cpp
DNABarcodes/src/barcode_set_distances.cpp
DNABarcodes/src/cachedistance.cpp
DNABarcodes/src/cachedistance.h
DNABarcodes/src/chromosome.cpp
DNABarcodes/src/chromosome.h
DNABarcodes/src/code_falsification.cpp
DNABarcodes/src/conway.cpp
DNABarcodes/src/conway.h
DNABarcodes/src/create_distance_func.cpp
DNABarcodes/src/create_distance_func.h
DNABarcodes/src/create_dnabarcodes.cpp
DNABarcodes/src/create_pool.cpp
DNABarcodes/src/demultiplex.cpp
DNABarcodes/src/distance.h
DNABarcodes/src/distance_for_R.cpp
DNABarcodes/src/genericchromosome.cpp
DNABarcodes/src/genericchromosome.h
DNABarcodes/src/greedyevolution.cpp
DNABarcodes/src/greedyevolution.h
DNABarcodes/src/hammingdistance.cpp
DNABarcodes/src/hammingdistance.h
DNABarcodes/src/helpers.cpp
DNABarcodes/src/helpers.h
DNABarcodes/src/levenshteindistance.cpp
DNABarcodes/src/levenshteindistance.h
DNABarcodes/src/maxclique.h
DNABarcodes/src/maxclique_pattabiraman_heuristic.cpp
DNABarcodes/src/maxclique_pattabiraman_heuristic.h
DNABarcodes/src/phaseshiftdist.cpp
DNABarcodes/src/phaseshiftdist.h
DNABarcodes/src/sequence.cpp
DNABarcodes/src/sequence.h
DNABarcodes/src/sequencelevenshteindistance.cpp
DNABarcodes/src/sequencelevenshteindistance.h
DNABarcodes/src/sequencepool.cpp
DNABarcodes/src/sequencepool.h
DNABarcodes/vignettes
DNABarcodes/vignettes/DNABarcodes.Rmd

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