Package: demuxSNP
Title: scRNAseq demultiplexing using cell hashing and SNPs
Version: 1.9.0
Authors@R: c(
    person("Michael", "Lynch", 
      email = "michael.lynch@ul.ie", 
      role = c("aut", "cre"),
      comment = c(ORCID = "0000-0001-9535-6461")),
    person("Aedin", "Culhane", 
      email = "aedin.culhane@ul.ie", 
      role = c("aut"), 
      comment = c(ORCID = "0000-0002-1395-9734")))
Description: 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.
URL: https://github.com/michaelplynch/demuxSNP
BugReports: https://github.com/michaelplynch/demuxSNP/issues
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation,
        ensembldb
Imports: MatrixGenerics, BiocGenerics, class, Seqinfo, IRanges, Matrix,
        SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr
Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr,
        dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat
        (>= 3.0.0), Seurat
biocViews: Classification, SingleCell
VignetteBuilder: knitr
LazyData: false
Config/testthat/edition: 3
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:23:27 UTC
RemoteUrl: https://github.com/bioc/demuxSNP
RemoteRef: HEAD
RemoteSha: e59403407a1ac2999cbfcceb02c75abbf3adf044
NeedsCompilation: no
Packaged: 2026-03-10 08:26:22 UTC; root
Author: Michael Lynch [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9535-6461>),
  Aedin Culhane [aut] (ORCID: <https://orcid.org/0000-0002-1395-9734>)
Maintainer: Michael Lynch <michael.lynch@ul.ie>
Built: R 4.6.0; ; 2026-03-10 08:29:49 UTC; windows
