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 (3.24)
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("demuxmix")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | demuxmix_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | demuxmix_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | demuxmix_1.15.0.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 |