hopach
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: Release (3.20)
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 "4.4") 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 | R Script | |
Reference Manual |
Details
biocViews | Clustering, Software |
Version | 2.66.0 |
In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 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, scClassify, treekoR |
Suggests Me | MicrobiotaProcess |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | hopach_2.66.0.tar.gz |
Windows Binary (x86_64) | hopach_2.66.0.zip |
macOS Binary (x86_64) | hopach_2.66.0.tgz |
macOS Binary (arm64) | hopach_2.65.0.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 |