This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see hopach.

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: 3.18

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")):


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

hopach PDF R Script
Reference Manual PDF


biocViews Clustering, Software
Version 2.62.0
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/
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Linking To
Depends On Me
Imports Me phenoTest, scClassify, treekoR
Suggests Me MicrobiotaProcess, seqArchR
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Package Archives

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

Source Package hopach_2.62.0.tar.gz
Windows Binary hopach_2.62.0.zip
macOS Binary (x86_64) hopach_2.62.0.tgz
macOS Binary (arm64) hopach_2.62.0.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/
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