clustComp
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see clustComp.
Clustering Comparison Package
Bioconductor version: 3.9
clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.
Author: Aurora Torrente and Alvis Brazma.
Maintainer: Aurora Torrente <aurora at ebi.ac.uk>
citation("clustComp")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clustComp")
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("clustComp")| The clustComp Package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3) |
| Imports | sm, stats, graphics, grDevices |
| System Requirements | |
| URL |
See More
| Suggests | Biobase, colonCA, RUnit, BiocGenerics |
| 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 | clustComp_1.12.0.tar.gz |
| Windows Binary | clustComp_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | clustComp_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/clustComp |
| Source Repository (Developer Access) | git clone [email protected]:packages/clustComp |
| Bioc Package Browser | https://code.bioconductor.org/browse/clustComp/ |
| Package Short Url | https://bioconductor.org/packages/clustComp/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |