To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("hopach")
In most cases, you don't need to download the package archive at all.
hopach
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: 3.0
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:
source("http://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")
| R Script | hopach | |
| Reference Manual |
Details
| biocViews | Clustering, Software |
| Version | 2.26.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| 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_2.26.0.tar.gz |
| Windows Binary | hopach_2.26.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | hopach_2.26.0.tgz |
| Mac OS X 10.9 (Mavericks) | hopach_2.26.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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