Package: demuxmix 1.7.0

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:Hans-Ulrich Klein [aut, cre]

demuxmix_1.7.0.tar.gz
demuxmix_1.7.0.zip(r-4.5)demuxmix_1.7.0.zip(r-4.4)demuxmix_1.7.0.zip(r-4.3)
demuxmix_1.7.0.tgz(r-4.4-any)demuxmix_1.7.0.tgz(r-4.3-any)
demuxmix_1.7.0.tar.gz(r-4.5-noble)demuxmix_1.7.0.tar.gz(r-4.4-noble)
demuxmix_1.7.0.tgz(r-4.4-emscripten)demuxmix_1.7.0.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

Datasets:

csf - Hashtag oligonucleotide (HTO) counts from 2,590 droplets

On BioConductor:demuxmix-1.7.0(bioc 3.20)demuxmix-1.6.0(bioc 3.19)

bioconductor-package

10 exports 0.91 score 29 dependencies 1 dependents

Last updated 2 months agofrom:f35ec72c4a

Exports:demuxmix dmmClassify dmmOverlap dmmSimulateHto pAcpt pAcpt<-plotDmmHistogram plotDmmPosteriorP plotDmmScatter summary

Dependencies:cli colorspace fansi farver ggplot2 glue gridExtra gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer rlang scales tibble utf8 vctrs viridisLite withr

Demultiplexing oligonucleotide-labeled scRNA-seq data with demuxmix

Hans-Ulrich Klein

Rendered fromdemuxmix.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2022-09-07
Started: 2021-08-08

Citation

Development and contributors

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