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 (3.21)
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:
Maintainer: Hans-Ulrich Klein <hansulrich.klein at gmail.com>
citation("demuxmix")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Preprocessing, Regression, Sequencing, SingleCell, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | demuxmix_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | demuxmix_1.9.0.tgz |
| macOS Binary (arm64) | demuxmix_1.9.0.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 |