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
git_url:
        https://git.bioconductor.org/packages/SingleCellAlleleExperiment
git_branch: RELEASE_3_22
git_last_commit: f2f4799
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 05:34:30 UTC; biocbuild
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 4.5.1; ; 2025-10-30 12:40:13 UTC; unix
