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BubbleTree

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

Bioconductor version: Release (3.17)

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 "4.3") 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 2.30.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 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
Linking To
Suggests knitr, rmarkdown
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Package Archives

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

Source Package BubbleTree_2.30.0.tar.gz
Windows Binary BubbleTree_2.30.0.zip
macOS Binary (x86_64) BubbleTree_2.30.0.tgz
macOS Binary (arm64) BubbleTree_2.30.0.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