DOI: 10.18129/B9.bioc.hopach  

This is the development version of hopach; for the stable release version, see hopach.

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: Development (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")):


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PDF R Script hopach
PDF   Reference Manual


biocViews Clustering, Software
Version 2.61.0
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
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
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Source Package hopach_2.61.0.tar.gz
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