To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HCsnip")
In most cases, you don't need to download the package archive at all.
HCsnip
|
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see HCsnip.
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Bioconductor version: 2.12
Decompose given hierarchical clustering tree into non-overlapping clusters in a semi-supervised way by using available patients follow-up information as guidance. Contains functions for snipping HC tree, various cluster quality evaluation criteria, assigning new patients to one of the two given HC trees, testing the significance of clusters with permutation argument and clusters visualization using sample's molecular entropy.
Author: Askar Obulkasim
Maintainer: Askar Obulkasim <askar.wubulikasimu at vumc.nl>
Citation (from within R,
enter citation("HCsnip")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HCsnip")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HCsnip")
| densityR.pdf | ||
| entropy.pdf | ||
| R Script | HCsnip | |
| Rank.pdf | ||
| Reference Manual |
Details
| biocViews | Bioinformatics, Clustering, GeneExpression, Microarray, Software, aCGH |
| Version | 1.0.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | HCsnip_1.0.0.tar.gz |
| Windows Binary | HCsnip_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | HCsnip_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/HCsnip/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/HCsnip/ |
| Package Downloads Report | Download Stats |
Documentation »
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