To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

CopywriteR

 

   

Copy number information from targeted sequencing using off-target reads

Bioconductor version: Release (3.5)

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>

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

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 2.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2 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.

Package Source CopywriteR_2.8.0.tar.gz
Windows Binary CopywriteR_2.8.0.zip
Mac OS X 10.11 (El Capitan) CopywriteR_2.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CopywriteR/tree/release-3.5
Package Short Url http://bioconductor.org/packages/CopywriteR/
Package Downloads Report Download Stats

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