Package: DeeDeeExperiment
Title: DeeDeeExperiment: An S4 Class for managing and exploring omics
        analysis results
Version: 1.3.0
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, writexl, 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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:05:18 UTC
RemoteUrl: https://github.com/bioc/DeeDeeExperiment
RemoteRef: HEAD
RemoteSha: 9bf542794ec216afcea72e63eb7a24b44a931e9a
NeedsCompilation: no
Packaged: 2026-06-09 10:25:03 UTC; root
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>