HCsnip

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("HCsnip")

Documentation

PDF R Script HCsnip
PDF   Reference Manual

Details

biocViews Clustering, GeneExpression, Microarray, Software, aCGH
Version 1.4.0
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 Downloads

Package Source HCsnip_1.4.0.tar.gz
Windows Binary HCsnip_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) HCsnip_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center