Package: DeeDeeExperiment
Title: DeeDeeExperiment: An S4 Class for managing and exploring omics
        analysis results
Version: 1.1.2
Authors@R: 
    c(
        person(
            given = "Najla", family = "Abassi", role = c("aut", "cre"), 
            email = "abassi.nejla96@gmail.com",
            comment = c(ORCID = "0000-0001-8357-0938")
        ),
        person(
            given = "Lea", family = "Schwarz", role = c("aut"),
            email = "lea.schwarz@uni-mainz.de",
            comment = c(ORCID = "0000-0003-2554-0583")
        ),
        person(
            given = "Federico", family = "Marini", role = c("aut"), 
            email = "marinif@uni-mainz.de",
            comment = c(ORCID = "0000-0003-3252-7758")
        )
    )
Description: DeeDeeExperiment is an S4 class extending the SingleCellExperiment
    class, designed to integrate and manage omics analysis results. It
    introduces two dedicated slots to store Differential Expression Analysis 
    (DEA) results and Functional Enrichment Analysis (FEA) results, providing a
    structured approach for downstream analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.5.0), SingleCellExperiment
Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2,
        edgeR, limma, cli
Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db,
        topGO, clusterProfiler, DEFormats, ExperimentHub, scater,
        muscat, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/imbeimainz/DeeDeeExperiment
BugReports: https://github.com/imbeimainz/DeeDeeExperiment/issues
biocViews: Software, Infrastructure, DataRepresentation,
        GeneExpression, Transcription, Transcriptomics,
        DifferentialExpression, Pathways, GO
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/DeeDeeExperiment
git_branch: devel
git_last_commit: c953024
git_last_commit_date: 2025-12-05
Repository: Bioconductor 3.23
Date/Publication: 2025-12-05
NeedsCompilation: no
Packaged: 2025-12-05 22:12:00 UTC; biocbuild
Author: Najla Abassi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8357-0938>),
  Lea Schwarz [aut] (ORCID: <https://orcid.org/0000-0003-2554-0583>),
  Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Najla Abassi <abassi.nejla96@gmail.com>
