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("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) | R Script | |
| Reference Manual | ||
| 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 | |
| URL |
See More
| Suggests | RUnit, NGScopyData, GenomicRanges |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]: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 |