Package: famat
Title: Functional analysis of metabolic and transcriptomic data
Version: 1.19.0
Description: 
    Famat is made to collect data about lists of genes and metabolites provided
    by user, and to visualize it through a Shiny app.
    Information collected is:
    - Pathways containing some of the user's genes and metabolites (obtained
    using a pathway enrichment analysis).
    - Direct interactions between user's elements inside pathways.
    - Information about elements (their identifiers and descriptions).
    - Go terms enrichment analysis performed on user's genes.
    The Shiny app is composed of:
    - information about genes, metabolites, and direct interactions between 
    them inside pathways.
    - an heatmap showing which elements from the list are in pathways 
    (pathways are structured in hierarchies).
    - hierarchies of enriched go terms using Molecular Function and 
    Biological Process.
Authors@R: 
    person(given = "Mathieu",
           family = "Charles",
           role = c("aut", "cre"),
           email = "mathieu.charles@inrae.fr",
           comment = c(ORCID = "0000-0001-5343-6324"))
License: GPL-3
LazyData: false
Depends: R (>= 4.0)
Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2,
        rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex,
        tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT,
        clusterProfiler, org.Hs.eg.db
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager
biocViews: FunctionalPrediction, GeneSetEnrichment, Pathways, GO,
        Reactome, KEGG
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
BugReports: https://github.com/emiliesecherre/famat/issues
URL: https://github.com/emiliesecherre/famat
git_url: https://git.bioconductor.org/packages/famat
git_branch: devel
git_last_commit: 3d31790
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 23:00:07 UTC; biocbuild
Author: Mathieu Charles [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5343-6324>)
Maintainer: Mathieu Charles <mathieu.charles@inrae.fr>
Built: R 4.5.0; ; 2025-06-05 12:57:58 UTC; windows
