Package: rScudo
Type: Package
Title: Signature-based Clustering for Diagnostic Purposes
Version: 1.24.0
Authors@R: c(person("Matteo", "Ciciani", email = "matteo.ciciani@gmail.com",
    role = c("aut", "cre")), person("Thomas", "Cantore",
    email = "cantorethomas@gmail.com", role = "aut"), person("Enrica",
    "Colasurdo", email = "enrica.colasurdo@gmail.com", role = "ctb"), person(
    "Mario", "Lauria", email = "mario.lauria@unitn.it", role = c("ctb")))
Description: SCUDO (Signature-based Clustering for Diagnostic Purposes) is a 
    rank-based method for the analysis of gene expression profiles for
    diagnostic and classification purposes. It is based on the identification of
    sample-specific gene signatures composed of the most up- and down-regulated
    genes for that sample. Starting from gene expression data, functions in this
    package identify sample-specific gene signatures and use them to build a
    graph of samples. In this graph samples are joined by edges if they have a
    similar expression profile, according to a pre-computed similarity matrix.
    The similarity between the expression profiles of two samples is computed
    using a method similar to GSEA. The graph of samples can then be used to
    perform community clustering or to perform supervised classification of
    samples in a testing set.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/Matteo-Ciciani/scudo
BugReports: https://github.com/Matteo-Ciciani/scudo/issues
Collate: 'class.R' 'accessors.R' 'packageDoc.R' 'utilities.R'
        'scudoClassifyUtilities.R' 'scudoClassify.R' 'scudoTrain.R'
        'scudoCytoscape.R' 'scudoModel.R' 'scudoNetwork.R'
        'scudoPlot.R' 'scudoTest.R' 'show.R'
RoxygenNote: 6.1.1
Depends: R (>= 3.6)
Imports: methods, stats, igraph, stringr, grDevices, Biobase,
        S4Vectors, SummarizedExperiment, BiocGenerics
Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
        e1071, parallel, doParallel
VignetteBuilder: knitr
biocViews: GeneExpression, DifferentialExpression,
        BiomedicalInformatics, Classification, Clustering,
        GraphAndNetwork, Network, Proteomics, Transcriptomics,
        SystemsBiology, FeatureExtraction
git_url: https://git.bioconductor.org/packages/rScudo
git_branch: RELEASE_3_21
git_last_commit: 3ea6f0e
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:28:37 UTC; biocbuild
Author: Matteo Ciciani [aut, cre],
  Thomas Cantore [aut],
  Enrica Colasurdo [ctb],
  Mario Lauria [ctb]
Maintainer: Matteo Ciciani <matteo.ciciani@gmail.com>
Built: R 4.5.0; ; 2025-04-16 06:24:52 UTC; unix
