HCsnip

DOI: 10.18129/B9.bioc.HCsnip    

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see HCsnip.

Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Bioconductor version: Release (3.6)

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 <askar703 at gmail.com>

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")

 

PDF	R Script	HCsnip
PDF		Reference Manual

Details

biocViews	Clustering, GeneExpression, Microarray, Software, aCGH
Version	1.17.0
In Bioconductor since	BioC 2.12 (R-3.0) (5 years)
License	GPL (>= 2)
Depends	R (>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase
Imports
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Depends On Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HCsnip_1.17.0.tar.gz
Windows Binary	HCsnip_1.17.0.zip
Mac OS X 10.11 (El Capitan)	HCsnip_1.17.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HCsnip
Package Short Url	http://bioconductor.org/packages/HCsnip/
Package Downloads Report	Download Stats