DESCRIPTION

Package: phenomis
Type: Package
Title: Analysis of single and multiple phenomic data sets
Version: 0.4.2
Date: 2022-06-03
Authors@R: c(
	   person(given = "Natacha", family = "Lenuzza",
	   email = "n.lenuzza@gmail.com",
	   role = "ctb"),
	   person(given = "Alyssa", family = "Imbert",
	   email = "alyssa.imbert@france-bioinformatique.fr",
	   role = "ctb"),
	   person(given = "Pierrick", family = "Roger",
	   email = "pierrick.roger@cea.fr",
	   role = "ctb"),
	   person(given = "Eric", family = "Venot",
	   email = "eric.venot@inrae.fr",
	   role = "ctb"),
	   person(given = "Sylvain", family = "Dechaumet",
	   email = "sylvain.dechaumet@cea.fr",
	   role = "ctb"),
	   person(given = "Etienne A.", family = "Thevenot",
	   email = "etienne.thevenot@cea.fr",
	   role = c("aut", "cre"),
	   comment = c(ORCID = "0000-0003-1019-4577"))
	   )
Author: Etienne A. Thevenot <etienne.thevenot@cea.fr>
Maintainer: Etienne A. Thevenot <etienne.thevenot@cea.fr>
Description: This package provides methods to perform the statistical analysis
    and integration of omics datasets (e.g. in metabolomics and proteomics).
    These methods include the reading of datasets into an 'ExpressionSet' object
    ('reading'), quality control ('inspecting'), transformation
    ('transforming') of the dataMatrix, and univariate hypothesis testing
    ('hypotesting'). Multivariate analysis, feature selection and annotation, can
    be further performed with the 'ropls', 'biosigner' and 'biodb' packages, as
    detailed in the vignette.
BiocViews:
    MassSpectrometry,
    Metabolomics,
    Normalization,
    StatisticalMethod,
    Clustering
Depends:
    SummarizedExperiment
Imports:
    Biobase,
    biodb,
    biodbChebi,
    biodbKegg,
    data.table,
    dplyr,
    futile.logger,
    ggplot2,
    ggrepel,
    graphics,
    grDevices,
    grid,
    htmlwidgets,
    igraph,
    limma,
    methods,
    MultiAssayExperiment,
    MultiDataSet,
    PMCMRplus,
    plotly,
    RColorBrewer,
    ropls,
    stats,
    tibble,
    tidyr,
    utils,
    VennDiagram
Suggests:
    BiocGenerics,
    BiocStyle,
    biosigner,
    knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr
License: CeCILL
Encoding: UTF-8
LazyData: true
URL: https://frama.link/etienne-thevenot
RoxygenNote: 7.2.0