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: 3.23 · Package version: 1.40.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ClusterSignificance")Details
| Maintainer | Jason T Serviss <jason.serviss@ki.se> |
| Author | Jason T. Serviss [aut, cre], Jesper R. Gadin [aut] |
| License | GPL-3 |
| URL | https://github.com/jasonserviss/ClusterSignificance/ |
| Bug Reports | https://github.com/jasonserviss/ClusterSignificance/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, Clustering, PrincipalComponent, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/ClusterSignificance/ |
Citation
From within R, enter citation("ClusterSignificance"):
Jason T. Serviss, Jesper R. Gadin. ClusterSignificance: The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. doi:10.18129/B9.bioc.ClusterSignificance, R package version 1.40.0, https://bioconductor.org/packages/ClusterSignificance.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ClusterSignificance_1.40.0.tar.gz |
| Windows binary (x86_64) | ClusterSignificance_1.40.0.zip |
| macOS binary (arm64) | ClusterSignificance_1.40.0.tgz |
| macOS binary (x86_64) | ClusterSignificance_1.40.0.tgz |
Dependencies
Depends: R (>= 3.3.0)
Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats
Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr