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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ClusterSignificance")
In most cases, you don't need to download the package archive at all.
ClusterSignificance
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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 (3.5)
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 and Jesper R. Gadin
Maintainer: Jason T Serviss <jason.serviss at ki.se>
Citation (from within R,
enter citation("ClusterSignificance")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ClusterSignificance")
Documentation
| HTML | R Script | ClusterSignificance Vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, PrincipalComponent, Software, StatisticalMethod |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.0) |
| Imports | methods, pracma, princurve, scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats |
| LinkingTo | |
| Suggests | knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClusterSignificance_1.4.1.tar.gz |
| Windows Binary | ClusterSignificance_1.4.1.zip |
| Mac OS X 10.11 (El Capitan) | ClusterSignificance_1.4.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClusterSignificance |
| Package Short Url | http://bioconductor.org/packages/ClusterSignificance/ |
| Package Downloads Report | Download Stats |
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