BubbleTree

This package is for version 3.14 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: 3.14

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Coverage, Sequencing, Software

Version 2.24.0

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

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Suggests knitr, rmarkdown

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Build Report Build Report

Package Archives

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

Source Package BubbleTree_2.24.0.tar.gz

Windows Binary BubbleTree_2.24.0.zip

macOS 10.13 (High Sierra) BubbleTree_2.24.0.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 3.14 Source Archive