CopywriteR

DOI: 10.18129/B9.bioc.CopywriteR    

Copy number information from targeted sequencing using off-target reads

Bioconductor version: Release (3.6)

CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

Author: Thomas Kuilman

Maintainer: Thomas Kuilman <t.kuilman at nki.nl>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CopywriteR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CopywriteR")

 

PDF	R Script	CopywriteR
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Coverage, ExomeSeq, Preprocessing, Software, TargetedResequencing, Visualization
Version	2.10.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	GPL-2
Depends	R (>= 3.2), BiocParallel
Imports	matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger
LinkingTo
Suggests	BiocStyle, SCLCBam, snow
SystemRequirements
Enhances
URL	https://github.com/PeeperLab/CopywriteR
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	CopywriteR_2.10.0.tar.gz
Windows Binary	CopywriteR_2.10.0.zip
Mac OS X 10.11 (El Capitan)	CopywriteR_2.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CopywriteR
Package Short Url	http://bioconductor.org/packages/CopywriteR/
Package Downloads Report	Download Stats