Introduction | Installation | Quick start | Demultiplexing droplets with demuxmix | Example datasets | Simulated dataset | Cell line mixture dataset | Running demuxmix | Quality control | Comparison to hashedDrops | Special usecase: pooling non-labeled with labeled cells | Session Info | References
Package: demuxmix 1.15.0
Hans-Ulrich Klein
demuxmix: Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.
Authors:
demuxmix_1.15.0.tar.gz
demuxmix_1.15.0.zip(r-4.7)demuxmix_1.15.0.zip(r-4.6)demuxmix_1.15.0.zip(r-4.5)
demuxmix_1.15.0.tgz(r-4.6-any)demuxmix_1.15.0.tgz(r-4.5-any)
demuxmix_1.15.0.tar.gz(r-4.7-any)demuxmix_1.15.0.tar.gz(r-4.6-any)
demuxmix_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
demuxmix/json (API)
| # Install 'demuxmix' in R: |
| install.packages('demuxmix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/huklein/demuxmix/issues
Datasets:
- csf - Hashtag oligonucleotide (HTO) counts from 2,590 droplets
On BioConductor:demuxmix-1.15.0(bioc 3.24)demuxmix-1.14.0(bioc 3.23)
singlecellsequencingpreprocessingclassificationregression
Last updated from:0375c4ecbb. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 200 | ||
| linux-devel-x86_64 | OK | 210 | ||
| source / vignettes | OK | 241 | ||
| linux-release-x86_64 | OK | 628 | ||
| macos-release-arm64 | OK | 97 | ||
| macos-oldrel-arm64 | OK | 106 | ||
| windows-devel | OK | 134 | ||
| windows-release | OK | 128 | ||
| windows-oldrel | OK | 136 | ||
| wasm-release | OK | 133 |
Exports:demuxmixdmmClassifydmmOverlapdmmSimulateHtopAcptpAcpt<-plotDmmHistogramplotDmmPosteriorPplotDmmScattersummary
Dependencies:clicpp11farverggplot2gluegridExtragtableisobandlabelinglatticelifecycleMASSMatrixR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Hashtag oligonucleotide (HTO) counts from 2,590 droplets | csf |
| Demultiplexing using mixture models | demuxmix demuxmix,Matrix,missing-method demuxmix,matrix,missing-method demuxmix,Matrix,numeric-method demuxmix,matrix,numeric-method |
| A class representing a set of mixture models fitted to HTO data | Demuxmix Demuxmix-class pAcpt pAcpt,Demuxmix-method pAcpt<- pAcpt<-,Demuxmix,numeric-method show,Demuxmix-method summary,Demuxmix-method |
| Return classification results from a Demuxmix object | dmmClassify dmmClassify,Demuxmix-method |
| Calculate the intersection of two components of a mixture model | dmmOverlap dmmOverlap,Demuxmix,ANY-method dmmOverlap,Demuxmix,missing-method |
| Simulate HTO sequencing data | dmmSimulateHto dmmSimulateHto,matrix-method |
| Plotting a histogram with mixture probability mass function | plotDmmHistogram plotDmmHistogram,Demuxmix,ANY-method plotDmmHistogram,Demuxmix,missing-method |
| Plotting a histogram of posterior probabilities | plotDmmPosteriorP plotDmmPosteriorP,Demuxmix,ANY-method plotDmmPosteriorP,Demuxmix,missing-method |
| Plotting RNA features versus HTO counts | plotDmmScatter plotDmmScatter,Demuxmix,ANY-method plotDmmScatter,Demuxmix,missing-method |
| Summarize classification results of a Demuxmix model | summary summary,data.frame-method |
