NGScopy

DOI: 10.18129/B9.bioc.NGScopy    

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see NGScopy.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("NGScopy")

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("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, ImmunoOncology, Sequencing, Software, TargetedResequencing, WholeGenome
Version	1.17.1
In Bioconductor since	BioC 3.0 (R-3.1) (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
Links To Me
Build Report

Package Archives

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

Source Package	NGScopy_1.17.1.tar.gz
Windows Binary	NGScopy_1.17.1.zip
Mac OS X 10.11 (El Capitan)	NGScopy_1.17.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NGScopy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NGScopy
Package Short Url	https://bioconductor.org/packages/NGScopy/
Package Downloads Report	Download Stats