DNABarcodes: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
Version 1.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorTilo Buschmann <tilo.buschmann.ac@gmail.com>
Bioconductor views Preprocessing Sequencing
Date of publicationNone
MaintainerTilo Buschmann <tilo.buschmann.ac@gmail.com>
LicenseGPL-2
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DNABarcodes")

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

Functions

DNABarcodes Man page
DNABarcodes-package Man page
analyse.barcodes Man page Source code
analyse_barcodes Source code
barcode.set.distances Man page Source code
barcode_set_distances Source code
code_falsification Source code
create.dnabarcodes Man page Source code
create.dnabarcodes.ashlock Man page Source code
create.dnabarcodes.clique Man page Source code
create.dnabarcodes.conway Man page Source code
create.dnabarcodes.sampling Man page Source code
create.pool Man page Source code
create_dnabarcodes Source code
create_pool Source code
demultiplex Man page Source code Source code
distance Man page Source code Source code
mutatedReads Man page
supplierSet Man page
test.code.falsification Source code
test_distance Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/analyse.barcodes.R
R/barcode.set.distances.R
R/create.dnabarcodes.R
R/create.pool.R
R/demultiplex.R
R/distance.R
R/test.code.falsification.R
build
build/vignette.rds
data
data/mutatedReads.rda
data/supplierSet.rda
inst
inst/CITATION
inst/doc
inst/doc/DNABarcodes.R
inst/doc/DNABarcodes.Rmd
inst/doc/DNABarcodes.html
man
man/DNABarcodes-package.Rd
man/analyse.barcodes.Rd
man/barcode.set.distances.Rd
man/create.dnabarcodes.Rd
man/create.pool.Rd
man/demultiplex.Rd
man/distance.Rd
man/mutatedReads.Rd
man/supplierSet.Rd
src
src/DNABarcodes_init.c
src/Makevars
src/RcppExports.cpp
src/analyse_barcodes.cpp
src/barcode_set_distances.cpp
src/cachedistance.cpp
src/cachedistance.h
src/chromosome.cpp
src/chromosome.h
src/code_falsification.cpp
src/conway.cpp
src/conway.h
src/create_distance_func.cpp
src/create_distance_func.h
src/create_dnabarcodes.cpp
src/create_pool.cpp
src/demultiplex.cpp
src/distance.h
src/distance_for_R.cpp
src/genericchromosome.cpp
src/genericchromosome.h
src/greedyevolution.cpp
src/greedyevolution.h
src/hammingdistance.cpp
src/hammingdistance.h
src/helpers.cpp
src/helpers.h
src/levenshteindistance.cpp
src/levenshteindistance.h
src/maxclique.h
src/maxclique_pattabiraman_heuristic.cpp
src/maxclique_pattabiraman_heuristic.h
src/phaseshiftdist.cpp
src/phaseshiftdist.h
src/sequence.cpp
src/sequence.h
src/sequencelevenshteindistance.cpp
src/sequencelevenshteindistance.h
src/sequencepool.cpp
src/sequencepool.h
vignettes
vignettes/DNABarcodes.Rmd
DNABarcodes documentation built on May 20, 2017, 10:35 p.m.