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demuxSNP

This is the development version of demuxSNP; to use it, please install the devel version of Bioconductor.

scRNAseq demultiplexing using cell hashing and SNPs

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews Classification, SingleCell, Software
Version 0.99.15
In Bioconductor since BioC 3.18 (R-4.3)
License GPL-3
Depends R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb
Imports MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, combinat
Linking To
Suggests knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/michaelplynch/demuxSNP
Bug Reports https://github.com/michaelplynch/demuxSNP/issues
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Build Report  

Package Archives

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

Source Package demuxSNP_0.99.15.tar.gz
Windows Binary demuxSNP_0.99.15.zip (64-bit only)
macOS Binary (x86_64) demuxSNP_0.99.15.tgz
macOS Binary (arm64) demuxSNP_0.99.15.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