demuxmix

DOI: 10.18129/B9.bioc.demuxmix  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see demuxmix.

Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models

Bioconductor version: 3.16

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.

Author: Hans-Ulrich Klein [aut, cre]

Maintainer: Hans-Ulrich Klein <hansulrich.klein at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("demuxmix")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("demuxmix")

 

HTML	R Script	Demultiplexing cells with demuxmix
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Preprocessing, Regression, Sequencing, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.0.0)
Imports	stats, MASS, Matrix, ggplot2, gridExtra, methods
LinkingTo
Suggests	BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/huklein/demuxmix
BugReports	https://github.com/huklein/demuxmix/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	demuxmix_1.0.0.tar.gz
Windows Binary	demuxmix_1.0.0.zip
macOS Binary (x86_64)	demuxmix_1.0.0.tgz
macOS Binary (arm64)	demuxmix_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/demuxmix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/demuxmix
Bioc Package Browser	https://code.bioconductor.org/browse/demuxmix/
Package Short Url	https://bioconductor.org/packages/demuxmix/
Package Downloads Report	Download Stats