Package: SingleCellAlleleExperiment
Title: S4 Class for Single Cell Data with Allele and Functional Levels
        for Immune Genes
Version: 1.6.0
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
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:30:07 UTC
RemoteUrl: https://github.com/bioc/SingleCellAlleleExperiment
RemoteRef: RELEASE_3_22
RemoteSha: f2f4799e7104fd15f637b98f65a498ff0ac3c3c8
NeedsCompilation: no
Packaged: 2025-11-11 17:49:01 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>
Built: R 4.5.2; ; 2025-11-12 03:08:28 UTC; windows
