Package: demuxmix 1.9.0
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_1.9.0.tar.gz
demuxmix_1.9.0.zip(r-4.5)demuxmix_1.9.0.zip(r-4.4)demuxmix_1.9.0.zip(r-4.3)
demuxmix_1.9.0.tgz(r-4.4-any)demuxmix_1.9.0.tgz(r-4.3-any)
demuxmix_1.9.0.tar.gz(r-4.5-noble)demuxmix_1.9.0.tar.gz(r-4.4-noble)
demuxmix_1.9.0.tgz(r-4.4-emscripten)demuxmix_1.9.0.tgz(r-4.3-emscripten)
demuxmix.pdf |demuxmix.html✨
demuxmix/json (API)
NEWS
| # 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
- csf - Hashtag oligonucleotide (HTO) counts from 2,590 droplets
On BioConductor:demuxmix-1.9.0(bioc 3.21)demuxmix-1.8.0(bioc 3.20)
singlecellsequencingpreprocessingclassificationregression
Last updated 2 months agofrom:6169ab16d0. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | OK | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:demuxmixdmmClassifydmmOverlapdmmSimulateHtopAcptpAcpt<-plotDmmHistogramplotDmmPosteriorPplotDmmScattersummary
Dependencies:clicolorspacefansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
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 |
