ClusterSignificance

DOI: 10.18129/B9.bioc.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: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	ClusterSignificance Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, PrincipalComponent, Software, StatisticalMethod
Version	1.22.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 years)
License	GPL-3
Depends	R (>= 3.3.0)
Imports	methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr
SystemRequirements
Enhances
URL	https://github.com/jasonserviss/ClusterSignificance/
BugReports	https://github.com/jasonserviss/ClusterSignificance/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ClusterSignificance_1.22.0.tar.gz
Windows Binary	ClusterSignificance_1.22.0.zip
macOS 10.13 (High Sierra)	ClusterSignificance_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ClusterSignificance
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ClusterSignificance
Package Short Url	https://bioconductor.org/packages/ClusterSignificance/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive