source("http://bioconductor.org/biocLite.R")
biocLite("HCsnip")

HCsnip

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

Bioconductor version: 2.13

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:

source("http://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		densityR.pdf
PDF		entropy.pdf
PDF	R Script	HCsnip
PDF		Rank.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, Clustering, GeneExpression, Microarray, Software, aCGH
Version	1.2.0
In Bioconductor since	BioC 2.12 (R-3.0)
License	GPL (>= 2)
Depends	R (>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	HCsnip_1.2.0.tar.gz
Windows Binary	HCsnip_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	HCsnip_1.2.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats