Package: pRoloc
Type: Package
Title: A unifying bioinformatics framework for spatial proteomics
Version: 1.48.0
Authors@R: c(person(given = "Laurent", family = "Gatto",
                    email = "laurent.gatto@uclouvain.be",
                    role = "aut"),
             person(given = "Lisa", family ="Breckels",
                    email = "lms79@cam.ac.uk",
                    role = c("aut", "cre")),
             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"))
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, colorspace
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, umap
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
git_url: https://git.bioconductor.org/packages/pRoloc
git_branch: RELEASE_3_21
git_last_commit: 0732005
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-15 23:17:20 UTC; biocbuild
Author: Laurent Gatto [aut],
  Lisa Breckels [aut, cre],
  Thomas Burger [ctb],
  Samuel Wieczorek [ctb],
  Charlotte Hutchings [ctb],
  Oliver Crook [aut]
Maintainer: Lisa Breckels <lms79@cam.ac.uk>
Built: R 4.5.0; x86_64-apple-darwin20; 2025-04-16 06:20:37 UTC; unix
