breakpointR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

Find breakpoints in Strand-seq data

Bioconductor version: Development (3.24)

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

Author: David Porubsky, Ashley Sanders, Aaron Taudt

Maintainer: David Porubsky <david.porubsky at gmail.com>

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

David Porubsky, Ashley Sanders, Aaron Taudt. breakpointR: Find breakpoints in Strand-seq data. doi:10.18129/B9.bioc.breakpointR, R package version 1.31.0, https://bioconductor.org/packages/breakpointR.

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")

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

BiocManager::install("breakpointR")

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("breakpointR")

How to use breakpointR	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNASeq, Sequencing, SingleCell, Software
Version	1.31.0
In Bioconductor since	BioC 3.8 (R-3.5) (8 years)
License	file LICENSE
Depends	R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
Imports	methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach
System Requirements
URL	https://github.com/daewoooo/BreakPointR

Suggests	knitr, BiocStyle, testthat
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	breakpointR_1.31.0.tar.gz
Windows Binary (x86_64)	breakpointR_1.31.0.zip
macOS Binary (big-sur-x86_64)	breakpointR_1.31.0.tgz
macOS Binary (sonoma-arm64)	breakpointR_1.31.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/breakpointR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/breakpointR
Package Short Url	https://bioconductor.org/packages/breakpointR/
Package Downloads Report	Download Stats