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.

Author
Tilo Buschmann <tilo.buschmann.ac@gmail.com>
Date of publication
None
Maintainer
Tilo Buschmann <tilo.buschmann.ac@gmail.com>
License
GPL-2
Version
1.4.0

View on Bioconductor

Man pages

analyse.barcodes
Analyse Sets of Barcode
barcode.set.distances
Calculate distances between each barcode pair of a barcode...
create.dnabarcodes
Create a set of DNA barcodes using one of several heuristic...
create.pool
Create a pool of barcode candidates.
demultiplex
Demultiplex a set of reads.
distance
Calculate distance between two barcodes.
DNABarcodes-package
Create and analyse DNA barcode sets that are capable of error...
mutatedReads
Mock Set of Mutated Reads
supplierSet
Mock Set of DNA Barcodes

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