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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: