Package: DaparToolshed
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Version: 0.99.31
Date: 2026-03-30
Authors@R: c(
    person(given = "Samuel", family = "Wieczorek",
    email = "samuel.wieczorek@cea.fr", role = c("cre", "aut"),
    comment=c(ORCID="0000-0002-5016-1203")),
    person(given = "Thomas", family ="Burger",
    email = "thomas.burger@cea.fr", role = c("aut")),
    person(given = "Enora", family ="Fremy",
    email = "enora.fremy@cea.fr", role = c("ctb")),
    person(given = "Manon", family ="Gaudin",
    email = "manon.gaudin@cea.fr", role = c("ctb"))
    )
Description: The package DaparToolshed is a Bioconductor distributed R package which 
    provides all the necessary functions to analyze quantitative data from 
    label-free proteomics experiments. It is an update 
    of our previous package DAPAR and contains more 
    functions to analyze the data and 
    uses MultAssayExperiment and SummarizedExperiment data structures.
    Contrarily to most other similar R packages, it is endowed with rich and 
    user-friendly graphical interfaces, so that no programming skill is 
    required (see `Prostar` package).
URL: https://github.com/edyp-lab/DaparToolshed,
        https://edyp-lab.github.io/DaparToolshed/
BugReports: https://github.com/edyp-lab/DaparToolshed/issues
License: Artistic-2.0
Depends: R (>= 4.5.0)
Imports: BiocGenerics, matrixStats, S4Vectors, SummarizedExperiment,
        openxlsx, QFeatures (>= 1.16), methods, MsCoreUtils,
        AnnotationFilter, RColorBrewer, plotly, stats, utils, tibble,
        Matrix, stringr, graph, igraph, preprocessCore, dplyr
biocViews: Proteomics, Normalization, Preprocessing, MassSpectrometry,
        QualityControl, DataImport
Suggests: BiocManager, visNetwork, htmlwidgets, rhandsontable,
        shinyalert, shinyjs, sos, knitr, shinyBS, MultiAssayExperiment,
        PSMatch, lme4, DT, shinyWidgets, vsn, cp4p, limma, imp4p (>=
        0.9), impute, apcluster, diptest, cluster, rmarkdown,
        BiocStyle, testthat, FactoMineR, factoextra, colourpicker,
        readxl, grDevices, forcats, multcomp, purrr, gplots, tidyr,
        Pirat, shinyjqui
NeedsCompilation: no
Collate: history_utils.R plots_volcano.R DiffAnalysis.R
        adjacencyMatrix.R plots_compare_assays.R
        missingValuesImputation_ProteinLevel.R
        missingValuesImputation_PeptideLevel.R hypothesisTest_plot.R
        anova_analysis.R compute.t.tests.R limmaAnalysis.R
        plots_normalization.R funcs_FunctionFiltering.R plot_metacell.R
        funcs_normalize.R doc-data.R QFeatures_utils.R output2Excel.R
        DaparToolshed_Params_Addons.R metacell.R
        DaparToolshed_filter_Adjmat.R DaparToolshed_QFeatures_Addons.R
        DaparToolshed_filter_qMetadata.R
        DaparToolshed-filterFeaturesOneSE.R export_qfeatures.R
        import_2_qfeatures.R utils.R pepa.R global.R initialization.R
        palette.R shinyValue.R get_pep_prot_cc.R aggregation.R
        heatmap.R zzz.R
RoxygenNote: 7.3.3
Packaged: 2026-04-09 06:04:59 UTC; pkgbuild
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Author: Samuel Wieczorek [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-5016-1203>),
  Thomas Burger [aut],
  Enora Fremy [ctb],
  Manon Gaudin [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
