- Home
- Bioconductor 3.4
- Software Packages
- NGScopy
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 3.4 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: 3.4
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")
| R Script | NGScopy: Detection of copy number variations in next generation sequencing (User's Guide) | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, DNASeq, ExomeSeq, Sequencing, Software, TargetedResequencing, WholeGenome |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 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_1.8.0.tar.gz |
| Windows Binary | NGScopy_1.8.0.zip |
| Mac OS X 10.9 (Mavericks) | NGScopy_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/NGScopy/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/NGScopy/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
