Package: rScudo
Type: Package
Title: Signature-based Clustering for Diagnostic Purposes
Version: 1.29.0
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
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:49:16 UTC
RemoteUrl: https://github.com/bioc/rScudo
RemoteRef: HEAD
RemoteSha: d9887b333d832625acb5cba3e00ea338b9a822c8
NeedsCompilation: no
Packaged: 2026-07-03 18:46:52 UTC; root
Author: Matteo Ciciani [aut, cre],
  Thomas Cantore [aut],
  Enrica Colasurdo [ctb],
  Mario Lauria [ctb]
Maintainer: Matteo Ciciani <matteo.ciciani@gmail.com>