Package: DAPAR
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Description: The package DAPAR is a Bioconductor distributed R package which 
    provides all the necessary functions to analyze quantitative data from 
    label-free proteomics experiments. 
    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).
Version: 1.43.0
Date: 2024-01-17
Author: c(person(given = "Samuel", family = "Wieczorek",
            email = "samuel.wieczorek@cea.fr", role = c("aut","cre")),
            person(given = "Florence", family ="Combes",
            email = "florence.combes@cea.fr", role = "aut"),
            person(given = "Thomas", family ="Burger",
            email = "thomas.burger@cea.fr", role = "aut"),
            person(given = "Vasile-Cosmin", family ="Lazar",
            email = "vcosminlazar@gmail.com", role = "ctb"),
		        person(given = "Enora", family ="Fremy",
            email = "enora.fremy@cea.fr", role = "ctb"),
    	      person(given = "Helene", family ="Borges",
            email = "helene.borges@cea.fr", role = "ctb"))
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
License: Artistic-2.0
VignetteBuilder: knitr
Depends: R (>= 4.3.0)
Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph,
        diptest, cluster, vioplot, visNetwork, vsn, igraph,  
        FactoMineR, factoextra, dendextend, parallel, doParallel, 
        Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble,
        knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4,
        dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots,
        grDevices, reshape2, graphics, stats, methods, ggplot2, 
        RColorBrewer, Matrix, org.Sc.sgd.db
Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach
biocViews: Proteomics, Normalization, Preprocessing, MassSpectrometry,
        QualityControl, GO, DataImport
NeedsCompilation: no
RoxygenNote: 7.3.1
Packaged: 2017-10-13 11:13:04 UTC; sw175264
Encoding: UTF-8
URL: http://www.prostar-proteomics.org/
BugReports: https://github.com/edyp-lab/DAPAR/issues
Collate:
    agregation.R
    anova_analysis.R
    bioAnalysis.R
    clustering.R
    dataset_Validity.R
    compute.t.tests.R
    DiffAnalysis.R
    get_pep_prot_cc.R
    metacell.R
    inOutFiles.R
    limmaAnalysis.R
    logText.R
    missingValuesFilter.R
    missingValuesImputation_PeptideLevel.R
    missingValuesImputation_ProteinLevel.R
    normalize.R
    pepa.R
    plots_boxplot.R
    plots_compare_Norm.R
    plots_corr_matrix.R
    plots_density.R
    plots_density_CV.R
    plots_heatmaps.R
    plots_pca.R
    plots_violin.R
    utils.R
    volcanoPlot.R
    palette.R
    hypothesisTest.R
    metacell_Plots.R
    zzz.R
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: devel
git_last_commit: 47a1b73
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
