GeneBreak

This is the development version of GeneBreak; for the stable release version, see GeneBreak.

Gene Break Detection

Bioconductor version: Development (3.24)

Recurrent breakpoint gene detection on copy number aberration profiles.

Author: Evert van den Broek, Stef van Lieshout

Maintainer: Evert van den Broek <vandenbroek.evert at gmail.com>

Citation (from within R, enter citation("GeneBreak")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("GeneBreak")

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("GeneBreak")

GeneBreak	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DNASeq, Genetics, Sequencing, Software, Visualization, WholeGenome, aCGH
Version	1.43.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	GPL-2
Depends	R (>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
Imports	graphics, methods
System Requirements
URL	https://github.com/stefvanlieshout/GeneBreak

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Build Report	Build Report

Package Archives

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

Source Package	GeneBreak_1.43.0.tar.gz
Windows Binary (x86_64)	GeneBreak_1.43.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	GeneBreak_1.43.0.tgz
macOS Binary (sonoma-arm64)	GeneBreak_1.43.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeneBreak
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeneBreak
Bioc Package Browser	https://code.bioconductor.org/browse/GeneBreak/
Package Short Url	https://bioconductor.org/packages/GeneBreak/
Package Downloads Report	Download Stats