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

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, ImmunoOncology, Sequencing, Software, TargetedResequencing, WholeGenome
Version 1.17.1
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>=2)
Depends R (>= 3.1.0)
Imports methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0), changepoint (>= 2.1.1)
System Requirements
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Suggests RUnit, NGScopyData, GenomicRanges
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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
Bioc Package Browser https://code.bioconductor.org/browse/NGScopy/
Package Short Url https://bioconductor.org/packages/NGScopy/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive