Why streaming? | Which chunk size to use? | Overview of the streaming API | Streaming using default callbacks | Assumptions | Obtaining the callbacks | Running the demultiplexing | Displaying the result from streaming | Streaming the barcode table | Considerations about size of tables | Subsetting the frequency table | Writing to database | Streaming using custom callbacks | Desired properties | The state object | The loader | The archiver | Putting it all together | Verifying results | Reproducibility | Bibliography
Package: posDemux 1.1.0
Jakob Peder Pettersen
posDemux: Positional combinatorial sequence demultiplexer
Demultiplexing and filtering utilities intended for reads with combinatorial barcodes (i.e. PETRI-seq and SPLiT-seq). The demultiplexer algorithm uses the position of the segments to extract and compare the barcodes with the reference (whitelist). A Shiny application is provided to interactively select cutoffs for which barcode combinations to keep.
Authors:
posDemux_1.1.0.tar.gz
posDemux_1.1.0.zip(r-4.7-x86_64)posDemux_1.1.0.zip(r-4.7-arm64)posDemux_1.1.0.zip(r-4.6-x86_64)posDemux_1.1.0.zip(r-4.6-arm64)posDemux_1.1.0.zip(r-4.5-x86_64)
posDemux_1.1.0.tgz(r-4.6-x86_64)posDemux_1.1.0.tgz(r-4.6-arm64)posDemux_1.1.0.tgz(r-4.5-x86_64)posDemux_1.1.0.tgz(r-4.5-arm64)
posDemux_1.1.0.tar.gz(r-4.7-arm64)posDemux_1.1.0.tar.gz(r-4.7-x86_64)posDemux_1.1.0.tar.gz(r-4.6-arm64)posDemux_1.1.0.tar.gz(r-4.6-x86_64)
posDemux_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
posDemux/json (API)
| # Install 'posDemux' in R: |
| install.packages('posDemux', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yaccos/posdemux/issues
Pkgdown/docs site:https://yaccos.github.io
On BioConductor:posDemux-1.1.0(bioc 3.24)posDemux-1.0.0(bioc 3.23)
sequencematchingsequencingsoftwarernaseqcpp
Last updated from:156cae8422. Checks:1 NOTE, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 190 | ||
| linux-devel-arm64 | OK | 208 | ||
| linux-devel-x86_64 | OK | 340 | ||
| source / vignettes | OK | 277 | ||
| linux-release-arm64 | OK | 197 | ||
| linux-release-x86_64 | OK | 346 | ||
| macos-release-arm64 | OK | 187 | ||
| macos-release-x86_64 | OK | 308 | ||
| macos-oldrel-arm64 | OK | 176 | ||
| macos-oldrel-x86_64 | OK | 441 | ||
| windows-devel-arm64 | OK | 304 | ||
| windows-devel-x86_64 | OK | 271 | ||
| windows-release-arm64 | OK | 267 | ||
| windows-release-x86_64 | OK | 206 | ||
| windows-oldrel-x86_64 | OK | 221 | ||
| wasm-release | OK | 152 |
Exports:bc_to_freq_cutoffcombinatorial_demultiplexcreate_freq_tablecreate_summary_resfilter_demultiplex_resfreq_plotfreq_to_bc_cutoffinteractive_bc_cutoffknee_plotrow_matchstreaming_callbacksstreaming_demultiplex
Dependencies:assertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsbslibcachemcigarilloclicliprcodetoolscommonmarkcpp11crayondeldirdigestdplyrfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshtmltoolshttpuvhwriterinterpIRangesisobandjpegjquerylibjsonlitelabelinglambda.rlaterlatticelatticeExtralifecyclemagrittrMASSmemoisemimeotelpillarpkgconfigpngprettyunitsprogresspromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenreadrRhtslibrlangRsamtoolsS4VectorsS7sassscalesSeqinfoshinyShortReadsnowsourcetoolstibbletidyselecttzdbutf8vctrsviridisLitevroomwithrxtableXVector
Streaming data into the demultiplexer
Last update: 2026-01-21
Started: 2025-09-26
Introduction to combinatorial demultiplexing
Basics | When and why to use this package | Required knowledge | Limitations | Ways to interact with this package | Install posDemux | Asking for help | Citing posDemux | An example with PETRI-seq | Quick overview of the method | Sequence annotation | Data loading | Running the demultiplexer | Error correction | Filtering by barcode frequency | Exporting results | Reproducibility | Bibliography
Last update: 2025-12-17
Started: 2025-12-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert between cutoff types | bc_to_freq_cutoff freq_to_bc_cutoff |
| Combinatorial demultiplexer | combinatorial_demultiplex |
| Frequency table | create_freq_table |
| Create a summary of match filtering | create_summary_res print.demultiplex_filter_summary |
| Filter demultiplexed reads | filter_demultiplex_res |
| Diagnostic plots from demultiplexing | freq_plot knee_plot |
| Interactive cutoff selection | interactive_bc_cutoff |
| Row matching of tables | row_match |
| Suggested setup for FASTQ streaming | streaming_callbacks |
| Demultiplexing with streaming | streaming_demultiplex |