hopach

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see hopach.

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("hopach")

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("hopach")
hopach PDF R Script
Reference Manual PDF

Details

biocViews Clustering, Software
Version 2.40.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2)
Depends R (>= 2.11.0), cluster, Biobase, methods
Imports graphics, grDevices, stats, utils, BiocGenerics
System Requirements
URL http://www.stat.berkeley.edu/~laan/ http://docpollard.org/
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me phenoTest
Suggests Me BiocCaseStudies
Links To Me
Build Report Build Report

Package Archives

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

Source Package hopach_2.40.0.tar.gz
Windows Binary hopach_2.40.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) hopach_2.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hopach
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hopach
Package Short Url https://bioconductor.org/packages/hopach/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive