BubbleTree

DOI: 10.18129/B9.bioc.BubbleTree    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BubbleTree.

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

Bioconductor version: 3.8

CNV analysis in groups of tumor samples.

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

Maintainer: Todd Creasy <creasyt at medimmune.com>, Wei Zhu <weizhu365 at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BubbleTree")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("BubbleTree")

 

HTML	R Script	BubbleTree Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Coverage, Sequencing, Software
Version	2.12.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	LGPL (>= 3)
Depends	R (>= 3.3), IRanges, GenomicRanges, plyr, dplyr, magrittr
Imports	BiocGenerics(>= 0.7.5), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BubbleTree_2.12.0.tar.gz
Windows Binary	BubbleTree_2.12.0.zip
Mac OS X 10.11 (El Capitan)	BubbleTree_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BubbleTree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BubbleTree
Package Short Url	http://bioconductor.org/packages/BubbleTree/
Package Downloads Report	Download Stats