BubbleTree
This package is for version 3.9 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: 3.9
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("BubbleTree")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, Sequencing, Software |
| Version | 2.14.0 |
| 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(>= 0.7.5), 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_2.14.0.tar.gz |
| Windows Binary | BubbleTree_2.14.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | BubbleTree_2.14.0.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 3.9 | Source Archive |