ClusterSignificance

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ClusterSignificance.

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data


Bioconductor version: 3.11

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.

Author: Jason T. Serviss [aut, cre], Jesper R. Gadin [aut]

Maintainer: Jason T Serviss <jason.serviss at ki.se>

Citation (from within R, enter citation("ClusterSignificance")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ClusterSignificance")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ClusterSignificance")
ClusterSignificance Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, PrincipalComponent, Software, StatisticalMethod
Version 1.16.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 3.3.0)
Imports methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats
System Requirements
URL https://github.com/jasonserviss/ClusterSignificance/
Bug Reports https://github.com/jasonserviss/ClusterSignificance/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ClusterSignificance_1.16.0.tar.gz
Windows Binary ClusterSignificance_1.16.0.zip
macOS 10.13 (High Sierra) ClusterSignificance_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ClusterSignificance
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ClusterSignificance
Bioc Package Browser https://code.bioconductor.org/browse/ClusterSignificance/
Package Short Url https://bioconductor.org/packages/ClusterSignificance/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive