BubbleTree

This package is for version 3.13 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: 3.13

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 "4.1") 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

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

browseVignettes("BubbleTree")
BubbleTree Tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Coverage, Sequencing, Software
Version 2.22.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License LGPL (>= 3)
Depends R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr
Imports BiocGenerics(>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils
System Requirements
URL
See More
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_2.22.0.tar.gz
Windows Binary BubbleTree_2.22.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) BubbleTree_2.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BubbleTree
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BubbleTree
Bioc Package Browser https://code.bioconductor.org/browse/BubbleTree/
Package Short Url https://bioconductor.org/packages/BubbleTree/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive