hopach
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see hopach.
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: 3.16
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 "4.2") 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 | 2.58.0 |
| 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/ |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | phenoTest, scClassify, treekoR |
| Suggests Me | MicrobiotaProcess, seqArchR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hopach_2.58.0.tar.gz |
| Windows Binary | hopach_2.58.0.zip (64-bit only) |
| macOS Binary (x86_64) | hopach_2.58.0.tgz |
| macOS Binary (arm64) | hopach_2.58.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |