Package: posDemux 1.0.0
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_1.0.0.tar.gz
posDemux_1.0.0.zip(r-4.7)posDemux_1.0.0.zip(r-4.6)posDemux_1.0.0.zip(r-4.5)
posDemux_1.0.0.tgz(r-4.6-x86_64)posDemux_1.0.0.tgz(r-4.6-arm64)posDemux_1.0.0.tgz(r-4.5-x86_64)posDemux_1.0.0.tgz(r-4.5-arm64)
posDemux_1.0.0.tar.gz(r-4.7-arm64)posDemux_1.0.0.tar.gz(r-4.7-x86_64)posDemux_1.0.0.tar.gz(r-4.6-arm64)posDemux_1.0.0.tar.gz(r-4.6-x86_64)
posDemux_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
posDemux/json (API)
NEWS
| # Install 'posDemux' in R: |
| install.packages('posDemux', repos = c('https://bioc-release.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:053127fe94 (on RELEASE_3_23). Checks:1 NOTE, 3 ERROR, 10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 192 | ||
| linux-devel-arm64 | ERROR | 244 | ||
| linux-devel-x86_64 | ERROR | 298 | ||
| source / vignettes | OK | 265 | ||
| linux-release-arm64 | OK | 262 | ||
| linux-release-x86_64 | OK | 305 | ||
| macos-release-arm64 | OK | 193 | ||
| macos-release-x86_64 | OK | 378 | ||
| macos-oldrel-arm64 | OK | 139 | ||
| macos-oldrel-x86_64 | OK | 492 | ||
| windows-devel | ERROR | 214 | ||
| windows-release | OK | 248 | ||
| windows-oldrel | OK | 221 | ||
| wasm-release | OK | 168 |
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
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 |
