Package: EMMA
Title: EMMA: Enrichment Methods Matter for enabling fully reproducible
        and provenance-aware pathway analysis
Version: 0.99.4
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 = "Annekathrin", family = "Nedwed", role = c("aut"),
            email = "anneludt@uni-mainz.de",
            comment = c(ORCID = "0000-0002-2475-4945")
        ),
        person(
            given = "Federico", family = "Marini", role = c("aut"), 
            email = "marinif@uni-mainz.de",
            comment = c(ORCID = "0000-0003-3252-7758")
        )
    )
Description: EMMA is a package that provides a provenance-aware
        execution framework for functional enrichment analyses. It
        allows users to run enrichment analyses using existing tools
        and workflows while explicitly capturing analytical parameters
        during runtime, and returns the native enrichment results
        output together with structured metadata.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
Imports: AnnotationDbi, cli
Suggests: knitr, rmarkdown, BiocStyle, macrophage, DESeq2, apeglm,
        clusterProfiler, gprofiler2, org.Hs.eg.db, GO.db, mosdef,
        topGO, renv, DeeDeeExperiment, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/imbeimainz/EMMA
BugReports: https://github.com/imbeimainz/EMMA/issues
biocViews: Software, Pathways, GO, KEGG, GeneSetEnrichment,
        ImmunoOncology, Transcriptomics, SingleCell, GeneExpression,
        DifferentialExpression
Config/testthat/edition: 3
Config/pak/sysreqs: libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-10 09:25:30 UTC
RemoteUrl: https://github.com/bioc/EMMA
RemoteRef: HEAD
RemoteSha: 7ac847ea2d30a263e366fb07b8161eaf6d5577a0
NeedsCompilation: no
Packaged: 2026-06-21 21:19:06 UTC; root
Author: Najla Abassi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8357-0938>),
  Annekathrin Nedwed [aut] (ORCID:
    <https://orcid.org/0000-0002-2475-4945>),
  Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Najla Abassi <abassi.nejla96@gmail.com>
Depends: R (>= 4.1.0)