Package: DAPAR
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Version: 1.22.9
Date: 2021-04-29
Authors@R: 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"))
Author: Samuel Wieczorek [cre,aut],
    Florence Combes [aut],
    Thomas Burger [aut],
    Cosmin Lazar [ctb],
    Alexia Dorffer [ctb],
    Anais Courtier [ctb],
    Helene Borges [ctb],
    Enora Fremy [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Description: This package contains a collection of functions for the
    visualisation and the statistical analysis of proteomic data.
License: Artistic-2.0
VignetteBuilder: knitr
Depends: R (>= 4.0.3)
Suggests: BiocGenerics, testthat, BiocStyle
Imports: Biobase, MSnbase, tibble, RColorBrewer,stats,preprocessCore,
        Cairo,png, lattice,reshape2,gplots,pcaMethods,ggplot2,
        limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics,
        openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot,
        imp4p (>= 0.8), forcats, methods, highcharter, DAPARdata (>=
        1.18.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr,
        tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra,
        multcomp, purrr, visNetwork, foreach, parallel, doParallel,
        igraph, dendextend, Mfuzz, apcluster, diptest, cluster
biocViews: Proteomics, Normalization, Preprocessing, MassSpectrometry,
        QualityControl, GO, DataImport
NeedsCompilation: no
RoxygenNote: 7.1.1
Packaged: 2021-04-30 23:02:18 UTC; biocbuild
Encoding: UTF-8
URL: http://www.prostar-proteomics.org/
BugReports: https://github.com/samWieczorek/DAPAR/issues
Collate: "agregation.R" "anova_analysis.R" "bioAnalysis.R"
        "clustering.R" "compute.t.tests.R" "DiffAnalysis.R"
        "get_pep_prot_cc.R" "inOutFiles.R" "limmaAnalysis.R"
        "logText.R" "missingValuesFilter.R"
        "missingValuesImputation_PeptideLevel.R"
        "missingValuesImputation_ProteinLevel.R" "missingValuesPlots.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"
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_12
git_last_commit: 0e5ad9b
git_last_commit_date: 2021-04-30
Date/Publication: 2021-04-30
Built: R 4.0.5; ; 2021-05-01 12:48:40 UTC; unix
