DESCRIPTION

Package: famat
Title: Functional analysis of metabolic and transcriptomic data
Version: 1.9.1
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