Package: DaparToolshed
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Version: 0.99.36
Date: 2026-05-07
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 palette.R
        shinyValue.R get_pep_prot_cc.R aggregation.R heatmap.R
        initialization.R
RoxygenNote: 7.3.3
Packaged: 2026-06-18 06:51:21 UTC; root
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-07 08:57:44 UTC
RemoteUrl: https://github.com/bioc/DaparToolshed
RemoteRef: HEAD
RemoteSha: dd69c315c69f443771cf70f41b7d57e3f11f259a
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>