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source("http://bioconductor.org/biocLite.R")
biocLite("NGScopy")
In most cases, you don't need to download the package archive at all.
NGScopy
NGScopy: Detection of copy number variations in next generation sequencing
Bioconductor version: 3.0
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:
source("http://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 | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>=2) |
| Depends | R (>= 3.1.0) |
| Imports | methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0), changepoint (>= 1.1.5) |
| 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_1.0.0.tar.gz |
| Windows Binary | NGScopy_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | NGScopy_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | NGScopy_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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