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scRNAseq demultiplexing using cell hashing and SNPs

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Classification, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Depends R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb
Imports MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr
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Suggests knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat
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Follow Installation instructions to use this package in your R session.

Source Package demuxSNP_1.2.0.tar.gz
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macOS Binary (x86_64) demuxSNP_1.2.0.tgz
macOS Binary (arm64) demuxSNP_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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