Package: SingleCellAlleleExperiment
Title: S4 Class for Single Cell Data with Allele and Functional Levels
        for Immune Genes
Version: 1.9.0
Authors@R: 
  c(
  person("Jonas", "Schuck", email="jschuckdev@gmail.com", role = c("aut", "cre"),
          comment = c(ORCID = "0009-0003-5705-4579")),
  person("Ahmad", "Al Ajami", role = c("aut"),
          comment = c(ORCID = "0009-0006-5615-7447")),
  person("Federico", "Marini", role = c("aut"),
          comment = c(ORCID = "0000-0003-3252-7758")),
  person("Katharina", "Imkeller", role = c("aut"),
          comment = c(ORCID = "0000-0002-5177-0852")))
Description: Defines a S4 class that is based on SingleCellExperiment.
        In addition to the usual gene layer the object can also store
        data for immune genes such as HLAs, Igs and KIRs at allele and
        functional level. The package is part of a workflow named
        single-cell ImmunoGenomic Diversity (scIGD), that firstly
        incorporates allele-aware quantification data for immune genes.
        This new data can then be used with the here implemented data
        structure and functionalities for further data handling and
        data analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0), SingleCellExperiment
Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods,
        utils, Matrix, S4Vectors, stats
Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater,
        scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi,
        DropletUtils, testthat (>= 3.0.0)
biocViews: DataRepresentation, Infrastructure, SingleCell,
        Transcriptomics, GeneExpression, Genetics, ImmunoOncology,
        DataImport
URL: https://github.com/AGImkeller/SingleCellAlleleExperiment
BugReports: https://github.com/AGImkeller/SingleCellAlleleExperiment/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:03:05 UTC
RemoteUrl: https://github.com/bioc/SingleCellAlleleExperiment
RemoteRef: HEAD
RemoteSha: 9fb15ed615ba18146b177d0275e670a2892e49a9
NeedsCompilation: no
Packaged: 2026-05-30 09:49:14 UTC; root
Author: Jonas Schuck [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-5705-4579>),
  Ahmad Al Ajami [aut] (ORCID: <https://orcid.org/0009-0006-5615-7447>),
  Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>),
  Katharina Imkeller [aut] (ORCID:
    <https://orcid.org/0000-0002-5177-0852>)
Maintainer: Jonas Schuck <jschuckdev@gmail.com>