demuxSNP
This is the development version of demuxSNP; for the stable release version, see demuxSNP.
scRNAseq demultiplexing using cell hashing and SNPs
Bioconductor version: Development (3.24)
This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.
Author: Michael Lynch [aut, cre]
, Aedin Culhane [aut]
Maintainer: Michael Lynch <michael.lynch at ul.ie>
citation("demuxSNP")):
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("demuxSNP")
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("demuxSNP")| Supervised Demultiplexing using Cell Hashing and SNPs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, SingleCell, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb |
| Imports | MatrixGenerics, BiocGenerics, class, Seqinfo, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr |
| System Requirements | |
| URL | https://github.com/michaelplynch/demuxSNP |
| Bug Reports | https://github.com/michaelplynch/demuxSNP/issues |
See More
| Suggests | knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | demuxSNP_1.11.0.tar.gz |
| Windows Binary (x86_64) | demuxSNP_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | demuxSNP_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | demuxSNP_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/demuxSNP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/demuxSNP |
| Bioc Package Browser | https://code.bioconductor.org/browse/demuxSNP/ |
| Package Short Url | https://bioconductor.org/packages/demuxSNP/ |
| Package Downloads Report | Download Stats |