Load the package | Define a helper function to save the raw dataset as a temporary text file | Design an experiment | Examples for single indexing | Examples for dual indexing | Build your own workflow | Load and check a dataset of barcodes | Examples of an exhaustive search of compatible barcode combinations | Examples of a random search of compatible barcode combinations | Constrain barcodes to be robust against one substitution error | Optimize the set of compatible combinations to reduce barcode redundancy | The optimized result isn't an optimum when filtering out too many barcodes
Package: DNABarcodeCompatibility 1.29.0
Céline Trébeau
DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
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.
Authors:
DNABarcodeCompatibility_1.29.0.tar.gz
DNABarcodeCompatibility_1.29.0.zip(r-4.7)DNABarcodeCompatibility_1.29.0.zip(r-4.6)DNABarcodeCompatibility_1.29.0.zip(r-4.5)
DNABarcodeCompatibility_1.29.0.tgz(r-4.6-x86_64)DNABarcodeCompatibility_1.29.0.tgz(r-4.6-arm64)DNABarcodeCompatibility_1.29.0.tgz(r-4.5-x86_64)DNABarcodeCompatibility_1.29.0.tgz(r-4.5-arm64)
DNABarcodeCompatibility_1.29.0.tar.gz(r-4.7-arm64)DNABarcodeCompatibility_1.29.0.tar.gz(r-4.7-x86_64)DNABarcodeCompatibility_1.29.0.tar.gz(r-4.6-arm64)DNABarcodeCompatibility_1.29.0.tar.gz(r-4.6-x86_64)
DNABarcodeCompatibility_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DNABarcodeCompatibility/json (API)
| # Install 'DNABarcodeCompatibility' in R: |
| install.packages('DNABarcodeCompatibility', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- IlluminaIndexes - Barcode dataset from Illumina with features.
- IlluminaIndexesRaw - Barcode dataset from Illumina.
On BioConductor:DNABarcodeCompatibility-1.29.0(bioc 3.24)DNABarcodeCompatibility-1.28.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:14bac8025e. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 167 | ||
| linux-devel-arm64 | NOTE | 192 | ||
| linux-devel-x86_64 | NOTE | 203 | ||
| source / vignettes | OK | 300 | ||
| linux-release-arm64 | NOTE | 219 | ||
| linux-release-x86_64 | NOTE | 190 | ||
| macos-release-arm64 | NOTE | 94 | ||
| macos-release-x86_64 | NOTE | 229 | ||
| macos-oldrel-arm64 | NOTE | 94 | ||
| macos-oldrel-x86_64 | NOTE | 314 | ||
| windows-devel | NOTE | 154 | ||
| windows-release | NOTE | 141 | ||
| windows-oldrel | NOTE | 142 | ||
| wasm-release | OK | 169 |
Exports:distancedistance_filterexperiment_designfile_loading_and_checkingget_all_combinationsget_random_combinationsoptimize_combinations
Dependencies:BHclicpp11dplyrgenericsgluelifecyclemagrittrnumberspillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DNABarcodeCompatibility: to find optimised sets of compatible barcodes with least heterogeneity in barcode usage for multiplex experiments performed on next generation sequencing platforms. | DNABarcodeCompatibility-package |
| Calculate distance between two barcodes. | distance |
| Select barcode combinations with error correction properties | distance_filter |
| Find a set of barcode combinations with least heterogeneity in barcode usage for single and dual indexing | experiment_design |
| Loading and checking DNA barcodes. | file_loading_and_checking |
| Get all compatible combinations. | get_all_combinations |
| Get a large set of compatible combinations. | get_random_combinations |
| Barcode dataset from Illumina with features. | IlluminaIndexes |
| Barcode dataset from Illumina. | IlluminaIndexesRaw |
| Find a set of barcode combinations with least heterogeneity in barcode usage | optimize_combinations |
