To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BubbleTree")

In most cases, you don't need to download the package archive at all.

BubbleTree

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see BubbleTree.

A method to elucidate purity and clonality in tumors using copy number ratio and allele frequency

Bioconductor version: 3.1

BubbleTree utilizes homogenous pertinent somatic copy number alterations (SCNAs) as markers of tumor clones to extract estimates of tumor ploidy, purity and clonality.

Author: Wei Zhu <zhuw at medimmune.com> Michael Kuziora <kuzioram at medimmune.com> Brandon Higgs <higgsb at medimmune.com>

Maintainer: Wei Zhu <zhuw at medimmune.com>

Citation (from within R, enter citation("BubbleTree")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BubbleTree")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BubbleTree")

 

HTML R Script BubbleTree Package Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Software
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License GPL (>=3.1)
Depends R (>= 3.0)
Imports GenomicRanges, IRanges, plyr, geosphere, mixdist, dplyr, shape
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
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 BubbleTree_1.0.0.tar.gz
Windows Binary BubbleTree_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) BubbleTree_1.0.0.tgz
Mac OS X 10.9 (Mavericks) BubbleTree_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BubbleTree/tree/release-3.1
Package Short Url http://bioconductor.org/packages/BubbleTree/
Package Downloads Report Download Stats

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