hopach

DOI: 10.18129/B9.bioc.hopach  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see hopach.

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

PDF	R Script	hopach
PDF		Reference Manual

Details

biocViews	Clustering, Software
Version	2.60.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License	GPL (>= 2)
Depends	R (>= 2.11.0), cluster, Biobase, methods
Imports	graphics, grDevices, stats, utils, BiocGenerics
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://www.stat.berkeley.edu/~laan/ http://docpollard.org/
Depends On Me
Imports Me	phenoTest, scClassify, treekoR
Suggests Me	MicrobiotaProcess, seqArchR
Links To Me
Build Report

Package Archives

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

Source Package	hopach_2.60.0.tar.gz
Windows Binary	hopach_2.60.0.zip (64-bit only)
macOS Binary (x86_64)	hopach_2.60.0.tgz
macOS Binary (arm64)	hopach_2.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/hopach
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hopach
Bioc Package Browser	https://code.bioconductor.org/browse/hopach/
Package Short Url	https://bioconductor.org/packages/hopach/
Package Downloads Report	Download Stats