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:Jakob Peder Pettersen [aut, cre], Centre for new antibacterial strategies [fnd]

posDemux_1.1.0.tar.gz
posDemux_1.1.0.zip(r-4.7)posDemux_1.1.0.zip(r-4.6)posDemux_1.1.0.zip(r-4.5)
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

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:posDemux-1.1.0(bioc 3.24)posDemux-1.0.0(bioc 3.23)

sequencematchingsequencingsoftwarernaseqcpp

5.11 score 7 scripts 12 exports 100 dependencies

Last updated from:156cae8422. Checks:1 NOTE, 3 ERROR, 10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE168
linux-devel-arm64ERROR269
linux-devel-x86_64ERROR322
source / vignettesOK295
linux-release-arm64OK272
linux-release-x86_64OK320
macos-release-arm64OK166
macos-release-x86_64OK284
macos-oldrel-arm64OK152
macos-oldrel-x86_64OK355
windows-develERROR273
windows-releaseOK247
windows-oldrelOK267
wasm-releaseOK201

Exports:bc_to_freq_cutoffcombinatorial_demultiplexcreate_freq_tablecreate_summary_resfilter_demultiplex_resfreq_plotfreq_to_bc_cutoffinteractive_bc_cutoffknee_plotrow_matchstreaming_callbacksstreaming_demultiplex

Dependencies:abindassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsbslibcachemcigarilloclicliprcodetoolscommonmarkcpp11crayonDelayedArraydeldirdigestdplyrfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshtmltoolshttpuvhwriterinterpIRangesisobandjpegjquerylibjsonlitelabelinglambda.rlaterlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeotelpillarpkgconfigpngprettyunitsprogresspromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsS7sassscalesSeqinfoshinyShortReadsnowsourcetoolsSparseArraySummarizedExperimenttibbletidyselecttzdbutf8vctrsviridisLitevroomwithrxtableXVector

Streaming data into the demultiplexer
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
Rendered fromstreaming.Rmdusingknitr::rmarkdown

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
Rendered fromposDemux.Rmdusingknitr::rmarkdown

Last update: 2025-12-17
Started: 2025-12-17

Readme and manuals

Help Manual

Help pageTopics
Convert between cutoff typesbc_to_freq_cutoff freq_to_bc_cutoff
Combinatorial demultiplexercombinatorial_demultiplex
Frequency tablecreate_freq_table
Create a summary of match filteringcreate_summary_res print.demultiplex_filter_summary
Filter demultiplexed readsfilter_demultiplex_res
Diagnostic plots from demultiplexingfreq_plot knee_plot
Interactive cutoff selectioninteractive_bc_cutoff
Row matching of tablesrow_match
Suggested setup for FASTQ streamingstreaming_callbacks
Demultiplexing with streamingstreaming_demultiplex