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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
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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 |
| 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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