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: 1.29.0
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
git_url: https://git.bioconductor.org/packages/ClusterSignificance
git_branch: devel
git_last_commit: 5ddd92a
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-26
Packaged: 2023-04-26 21:53:26 UTC; biocbuild
Built: R 4.3.0; ; 2023-04-27 11:31:02 UTC; windows
