Package: famat
Title: Functional analysis of metabolic and transcriptomic data
Version: 1.0.0
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 = "Emilie",
           family = "Secherre",
           role = c("aut", "cre"),
           email = "emisecherre@gmail.com",
           comment = c(ORCID = "0000-0001-5343-6324"))
License: GPL-3
LazyData: false
Depends: R (>= 4.0)
Imports: KEGGREST, MPINet, 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: RELEASE_3_12
git_last_commit: 6f56a8b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
NeedsCompilation: no
Packaged: 2020-10-28 00:09:44 UTC; biocbuild
Author: Emilie Secherre [aut, cre] (<https://orcid.org/0000-0001-5343-6324>)
Maintainer: Emilie Secherre <emisecherre@gmail.com>
Built: R 4.0.3; ; 2021-04-02 02:04:21 UTC; unix
