hopach
This is the development version of hopach; for the stable release version, see hopach.
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.73.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 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_2.73.0.tar.gz |
| Windows Binary (x86_64) | hopach_2.73.0.zip |
| macOS Binary (big-sur-x86_64) | hopach_2.73.0.tgz |
| macOS Binary (sonoma-arm64) | hopach_2.73.0.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 |