To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")
In most cases, you don't need to download the package archive at all.
hopach
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see hopach.
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: 3.2
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("hopach")
| hopach | ||
| Reference Manual |
Details
| biocViews | Clustering, Software |
| Version | 2.30.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 11 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.11.0), cluster, Biobase, methods |
| Imports | graphics, grDevices, stats, utils, BiocGenerics |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.stat.berkeley.edu/~laan/ http://docpollard.org/ |
| Depends On Me | |
| Imports Me | phenoTest |
| Suggests Me | BiocCaseStudies |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | hopach_2.30.0.tar.gz |
| Windows Binary | hopach_2.30.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | hopach_2.30.0.tgz |
| Mac OS X 10.9 (Mavericks) | hopach_2.30.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/hopach/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/hopach/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
