To install this package, start R and enter:

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

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

NGScopy

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see NGScopy.

NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing

Bioconductor version: 3.1

NGScopy provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer.

Author: Xiaobei Zhao [aut, cre, cph]

Maintainer: Xiaobei Zhao <xiaobei at binf.ku.dk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("NGScopy")
PDF R Script NGScopy: Detection of copy number variations in next generation sequencing (User's Guide)
PDF Reference Manual
Text NEWS

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Sequencing, Software, TargetedResequencing, WholeGenome
Version 1.2.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL (>=2)
Depends R (>= 3.1.0)
Imports methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0), changepoint (>= 2.1.1)
LinkingTo
Suggests RUnit, NGScopyData, GenomicRanges
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source NGScopy_1.2.2.tar.gz
Windows Binary NGScopy_1.2.2.zip
Mac OS X 10.6 (Snow Leopard) NGScopy_1.2.0.tgz
Mac OS X 10.9 (Mavericks) NGScopy_1.2.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/NGScopy/tree/release-3.1
Package Short Url http://bioconductor.org/packages/NGScopy/
Package Downloads Report Download Stats

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