hopach

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

Author Katherine S. Pollard, with Mark J. van der Laan .
Maintainer Katherine S. Pollard

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("hopach")

Vignettes (Documentation)

Package Downloads

MSS.pdf
bootplot.pdf
dplot.pdf
hopach.pdf
hopachManuscript.pdf
Source hopach_1.12.0.tar.gz
Windows binary hopach_1.12.0.zip
OS X binary hopach_1.12.0.tgz

Details

biocViews
Depends R, cluster, Biobase
Suggests
Imports
SystemRequirements
License GPL version 2 or newer
URL http://www.r-project.org, http://www.stat.berkeley.edu/~laan/, http://docpollard.com/
dependsOnMe
suggestsMe