BubbleTree

This package is for version 3.6 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: 3.6

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>

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

Installation

To install this package, start R (version "3.4") and enter:


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

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

Documentation

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Coverage, Sequencing, Software

Version 2.8.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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

System Requirements

URL

Suggests knitr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package BubbleTree_2.8.0.tar.gz

Windows Binary BubbleTree_2.8.0.zip

Mac OS X 10.11 (El Capitan) BubbleTree_2.8.0.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 https://bioconductor.org/packages/BubbleTree/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive