Package: DAPAR
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Version: 1.24.8
Date: 2021-08-19
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 (>= 4.1.0)
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 (>= 1.1), forcats, methods, DAPARdata (>= 1.22.2),
        siggenes, graph, lme4, readxl, highcharter, 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: 2021-08-22 17:53:01 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 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
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_13
git_last_commit: 4b52ffd
git_last_commit_date: 2021-08-19
Date/Publication: 2021-08-22
Built: R 4.1.0; ; 2021-08-23 13:29:45 UTC; windows
