demuxSNP

DOI: 10.18129/B9.bioc.demuxSNP  

scRNAseq demultiplexing using cell hashing and SNPs

Bioconductor version: Release (3.18)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Supervised Demultiplexing using Cell Hashing and SNPs
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb
Imports	MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, combinat
LinkingTo
Suggests	knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/michaelplynch/demuxSNP
BugReports	https://github.com/michaelplynch/demuxSNP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	demuxSNP_1.0.0.tar.gz
Windows Binary	demuxSNP_1.0.0.zip
macOS Binary (x86_64)	demuxSNP_1.0.0.tgz
macOS Binary (arm64)	demuxSNP_1.0.0.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
Old Source Packages for BioC 3.18	Source Archive