Package: demuxSNP
Title: scRNAseq demultiplexing using cell hashing and SNPs
Version: 1.0.0
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: 7.2.3
Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation,
        ensembldb
Imports: MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges,
        Matrix, SummarizedExperiment, demuxmix, methods, combinat
Suggests: knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite,
        ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR,
        testthat (>= 3.0.0)
biocViews: Classification, SingleCell
VignetteBuilder: knitr
LazyData: false
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/demuxSNP
git_branch: RELEASE_3_18
git_last_commit: 1af04e3
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 20:58:36 UTC; biocbuild
Author: Michael Lynch [aut, cre] (<https://orcid.org/0000-0001-9535-6461>),
  Aedin Culhane [aut] (<https://orcid.org/0000-0002-1395-9734>)
Maintainer: Michael Lynch <michael.lynch@ul.ie>
Built: R 4.3.2; ; 2023-12-09 20:05:46 UTC; unix
