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demuxmix

This is the development version of demuxmix; for the stable release version, see demuxmix.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("demuxmix")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, Preprocessing, Regression, Sequencing, SingleCell, Software
Version 1.5.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports stats, MASS, Matrix, ggplot2, gridExtra, methods
System Requirements
URL https://github.com/huklein/demuxmix
Bug Reports https://github.com/huklein/demuxmix/issues
See More
Suggests BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me demuxSNP
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package demuxmix_1.5.1.tar.gz
Windows Binary demuxmix_1.5.1.zip
macOS Binary (x86_64) demuxmix_1.5.1.tgz
macOS Binary (arm64) demuxmix_1.5.1.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