demuxmix

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see demuxmix.

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

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-6382-9428

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

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

Installation

To install this package, start R (version "4.5") 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")

Demultiplexing cells with demuxmix HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Preprocessing, Regression, Sequencing, SingleCell, Software

Version 1.10.0

In Bioconductor since BioC 3.16 (R-4.2) (3 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

Suggests BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0)

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Package Archives

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

Source Package demuxmix_1.10.0.tar.gz

Windows Binary (x86_64) demuxmix_1.10.0.zip (64-bit only)

macOS Binary (x86_64) demuxmix_1.10.0.tgz

macOS Binary (arm64) demuxmix_1.10.0.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/

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