Package: ClusterSignificance
Title: The ClusterSignificance package provides tools to assess if
        class clusters in dimensionality reduced data representations
        have a separation different from permuted data
Version: 1.39.0
Authors@R: c(
    person("Jason T.", "Serviss", email = "Jason.serviss@ki.se", role = c("aut", "cre"), comment = c(ORCID = 0000-0002-5778-7014)),
    person("Jesper R.", "Gadin", email = "Jesper.gadin@ki.se", role = c("aut"))
    )
Author: Jason T. Serviss [aut, cre], Jesper R. Gadin [aut]
Maintainer: Jason T Serviss <jason.serviss@ki.se>
Description: The ClusterSignificance package provides tools to assess
        if class clusters in dimensionality reduced data
        representations have a separation different from permuted data.
        The term class clusters here refers to, clusters of points
        representing known classes in the data. This is particularly
        useful to determine if a subset of the variables, e.g. genes in
        a specific pathway, alone can separate samples into these
        established classes. ClusterSignificance accomplishes this by,
        projecting all points onto a one dimensional line. Cluster
        separations are then scored and the probability of the seen
        separation being due to chance is evaluated using a permutation
        method.
Depends: R (>= 3.3.0)
URL: https://github.com/jasonserviss/ClusterSignificance/
BugReports: https://github.com/jasonserviss/ClusterSignificance/issues
Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d,
        RColorBrewer, grDevices, graphics, utils, stats
License: GPL-3
LazyData: true
Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
        covr
VignetteBuilder: knitr
biocViews: Clustering, Classification, PrincipalComponent,
        StatisticalMethod
NeedsCompilation: no
Collate: 'ClusterSignificance-package.R' 'All-classes.R'
        'classifier-methods.R' 'initialize-methods.R' 'mlpMatrix.R'
        'pcpMatrix.R' 'permutation-methods.R' 'plot-methods.R'
        'projection-methods.R' 'show-methods.R'
RoxygenNote: 6.0.1
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:31:54 UTC
RemoteUrl: https://github.com/bioc/ClusterSignificance
RemoteRef: HEAD
RemoteSha: ce3fb626d708412a238197ae8c806f231b9e9ceb
Packaged: 2025-11-02 03:35:15 UTC; root
Built: R 4.6.0; ; 2025-11-02 03:36:55 UTC; windows
