hopach
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see hopach.
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: 3.14
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("hopach")):
Installation
To install this package, start R (version "4.1") 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")
Details
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Follow Installation instructions to use this package in your R session.