Package: famat
Title: Functional analysis of metabolic and transcriptomic data
Version: 1.23.0
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 (>= 4.3)
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, ReactomePA, enrichplot
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:54:16 UTC
RemoteUrl: https://github.com/bioc/famat
RemoteRef: HEAD
RemoteSha: 58f2c76c9e944e317ef3a04799cdcdb4c8c9acb4
NeedsCompilation: no
Packaged: 2026-07-04 06:24:20 UTC; root
Author: Mathieu Charles [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5343-6324>)
Maintainer: Mathieu Charles <mathieu.charles@inrae.fr>