Using DNABarcodes | Creating a Pristine Set of DNA Barcodes | Sets with Larger Number of Correctable Errors | Sets of DNA Barcodes Capable of Correcting Insertions, Deletions, and Substitutions | Applying Different Filters | Subsetting an Existing Set of DNA Barcodes | Demultiplexing | Analysing a Set of DNA Barcodes | Distance Metrics | Set Generation Heuristics | Configuration of Ashlock Heuristic
Package: DNABarcodes 1.43.0
Tilo Buschmann
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.
Authors:
DNABarcodes_1.43.0.tar.gz
DNABarcodes_1.43.0.zip(r-4.7)DNABarcodes_1.43.0.zip(r-4.6)DNABarcodes_1.43.0.zip(r-4.5)
DNABarcodes_1.43.0.tgz(r-4.6-x86_64)DNABarcodes_1.43.0.tgz(r-4.6-arm64)DNABarcodes_1.43.0.tgz(r-4.5-x86_64)DNABarcodes_1.43.0.tgz(r-4.5-arm64)
DNABarcodes_1.43.0.tar.gz(r-4.7-arm64)DNABarcodes_1.43.0.tar.gz(r-4.7-x86_64)DNABarcodes_1.43.0.tar.gz(r-4.6-arm64)DNABarcodes_1.43.0.tar.gz(r-4.6-x86_64)
DNABarcodes_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DNABarcodes/json (API)
| # Install 'DNABarcodes' in R: |
| install.packages('DNABarcodes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- mutatedReads - Mock Set of Mutated Reads
- supplierSet - Mock Set of DNA Barcodes
On BioConductor:DNABarcodes-1.43.0(bioc 3.24)DNABarcodes-1.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
preprocessingsequencingcppopenmp
Last updated from:e69dd9e5dc. Checks:1 ERROR, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 177 | ||
| linux-devel-arm64 | OK | 178 | ||
| linux-devel-x86_64 | OK | 200 | ||
| source / vignettes | OK | 245 | ||
| linux-release-arm64 | OK | 191 | ||
| linux-release-x86_64 | OK | 209 | ||
| macos-release-arm64 | OK | 152 | ||
| macos-release-x86_64 | OK | 279 | ||
| macos-oldrel-arm64 | OK | 141 | ||
| macos-oldrel-x86_64 | OK | 400 | ||
| windows-devel | OK | 230 | ||
| windows-release | OK | 211 | ||
| windows-oldrel | OK | 177 | ||
| wasm-release | OK | 182 |
Exports:analyse.barcodesbarcode.set.distancescreate.dnabarcodescreate.dnabarcodes.ashlockcreate.dnabarcodes.cliquecreate.dnabarcodes.conwaycreate.dnabarcodes.samplingcreate.pooldemultiplexdistance
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create and analyse DNA barcode sets that are capable of error correction. | DNABarcodes-package DNABarcodes |
| Analyse Sets of Barcode | analyse.barcodes |
| Calculate distances between each barcode pair of a barcode set. | barcode.set.distances |
| Create a set of DNA barcodes using one of several heuristic methods. | create.dnabarcodes create.dnabarcodes.ashlock create.dnabarcodes.clique create.dnabarcodes.conway create.dnabarcodes.sampling |
| Create a pool of barcode candidates. | create.pool |
| Demultiplex a set of reads. | demultiplex |
| Calculate distance between two barcodes. | distance |
| Mock Set of Mutated Reads | mutatedReads |
| Mock Set of DNA Barcodes | supplierSet |
