BubbleTree
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last 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: Release (3.23)
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")):Wei Zhu, Michael Kuziora, Todd Creasy, Brandon Higgs. BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data. doi:10.18129/B9.bioc.BubbleTree, R package version 2.42.0, https://bioconductor.org/packages/BubbleTree.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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
| No vignettes available | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Coverage, Sequencing, Software |
| Version | 2.42.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 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 |
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |