DESCRIPTION

Package: pRoloc
Type: Package
Title: A unifying bioinformatics framework for spatial proteomics
Version: 1.45.2
Authors@R: c(person(given = "Laurent", family = "Gatto",
                    email = "laurent.gatto@uclouvain.be",
                    role = c("aut","cre")),
             person(given = "Lisa", family ="Breckels",
                    email = "lms79@cam.ac.uk",
                    role = "aut"),
             person(given = "Thomas", family ="Burger",
                    email = "Thomas.BURGER@cea.fr",
                    role = "ctb"),
             person(given = "Samuel", family ="Wieczorek",
                    email = "samuel.wieczorek@cea.fr",
                    role = "ctb"),
             person(given = "Charlotte", family ="Hutchings",
                    email = "ch941@cam.ac.uk",
                    role = "ctb"),
             person(given = "Oliver", family ="Crook",
                    email = "oliver.crook@stats.ox.ac.uk",
                    role = "aut"))
Author: Laurent Gatto, Oliver Crook and Lisa M. Breckels with
    contributions from Thomas Burger and Samuel Wieczorek
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
Description: The pRoloc package implements machine learning and
             visualisation methods for the analysis and interogation
             of quantitiative mass spectrometry data to reliably infer
             protein sub-cellular localisation.
Depends:
    R (>= 3.5),
    MSnbase (>= 1.19.20),
    MLInterfaces (>= 1.67.10),
    methods,
    Rcpp (>= 0.10.3),
    BiocParallel
Imports:
    stats4,
    Biobase,
    mclust (>= 4.3),
    caret,
    e1071,
    sampling,
    class,
    kernlab,
    lattice,
    nnet,
    randomForest,
    proxy,
    FNN,
    hexbin,
    BiocGenerics,
    stats,
    dendextend,
    RColorBrewer,
    scales,
    MASS,
    knitr,
    mvtnorm,
    LaplacesDemon,
    coda,
    mixtools,
    gtools,
    plyr,
    ggplot2,
    biomaRt,
    utils,
    grDevices,
    graphics
Suggests:
    testthat,
    rmarkdown,
    pRolocdata (>= 1.43.2),
    roxygen2,
    xtable,
    rgl,
    BiocStyle (>= 2.5.19),
    hpar (>= 1.41.0),
    dplyr,
    akima,
    fields,
    vegan,
    GO.db,
    AnnotationDbi,
    Rtsne (>= 0.13),
    nipals,
    reshape,
    magick
LinkingTo: Rcpp, RcppArmadillo
License: GPL-2
VignetteBuilder: knitr
Video: https://www.youtube.com/playlist?list=PLvIXxpatSLA2loV5Srs2VBpJIYUlVJ4ow
URL: https://github.com/lgatto/pRoloc
BugReports: https://github.com/lgatto/pRoloc/issues
biocViews: ImmunoOncology, Proteomics, MassSpectrometry, Classification, Clustering,
    QualityControl
Collate:
    AllGenerics.R
    machinelearning-framework.R
    machinelearning-framework-theta.R
    machinelearning-framework-map.R
    machinelearning-framework-mcmc.R
    machinelearning-utils.R
    machinelearning-functions-knn.R
    machinelearning-functions-ksvm.R
    machinelearning-functions-nb.R
    machinelearning-functions-nnet.R
    machinelearning-functions-PerTurbo.R
    machinelearning-functions-plsda.R
    machinelearning-functions-rf.R
    machinelearning-functions-svm.R
    machinelearning-functions-knntl.R
    machinelearning-functions-tagm-map.R
    machinelearning-functions-tagm-mcmc.R
    machinelearning-functions-tagm-mcmc-helper.R
    RcppExports.R
    belief.R
    distances.R
    markers.R
    pRolocmarkers.R
    chi2.R
    MLInterfaces.R
    clustering-framework.R
    MSnSet.R
    clustering-kmeans.R
    perTurbo-algorithm.R
    phenodisco.R
    plotting.R
    plotting2.R
    plotting3.R
    plottingBayes.R
    plotting-ellipse.R
    hclust.R
    environment.R
    utils.R
    annotation.R
    goenv.R
    go.R
    makeGoSet.R
    vis.R
    MartInterface.R
    dynamics.R
    zzz.R
    goannotations.R
    clusterdist-functions.R
    clusterdist-framework.R
    qsep.R
RoxygenNote: 7.3.2
Encoding: UTF-8