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Bioconductor - demuxSNP

demuxSNP

This is the released version of demuxSNP; for the devel version, see demuxSNP.

scRNAseq demultiplexing using cell hashing and SNPs

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-9535-6461 , Aedin Culhane [aut] ORCID: 0000-0002-1395-9734

Maintainer: Michael Lynch <michael.lynch at ul.ie>

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

To install this package, start R (version "4.5") 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")
Supervised Demultiplexing using Cell Hashing and SNPs HTML R Script Reference Manual PDF NEWS Text Details biocViews Classification, SingleCell, Software Version 1.6.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License GPL-3 Depends R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports MatrixGenerics, BiocGenerics, class, GenomeInfoDb, 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.

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