To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")

In most cases, you don't need to download the package archive at all.

hopach

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see hopach.

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: 2.12

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 <laan at stat.berkeley.edu> and Greg Wall

Maintainer: Katherine S. Pollard <katherine.pollard at gladstone.ucsf.edu>

Citation (from within R, enter citation("hopach")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("hopach")

PDF		bootplot.pdf
PDF		dplot.pdf
PDF	R Script	hopach
PDF		hopachManuscript.pdf
PDF		MSS.pdf
PDF		Reference Manual

Details

biocViews	Clustering, Software
Version	2.20.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 11 years)
License	GPL (>= 2)
Depends	R (>= 2.11.0), cluster, Biobase, methods
Imports	Biobase, cluster, graphics, grDevices, methods, stats, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://www.stat.berkeley.edu/~laan/ http://docpollard.org/
Depends On Me
Imports Me	phenoTest
Suggests Me	BiocCaseStudies
Build Report

Package Archives

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

Package Source	hopach_2.20.0.tar.gz
Windows Binary	hopach_2.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	hopach_2.20.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/hopach/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/hopach/
Package Downloads Report	Download Stats