source("http://bioconductor.org/biocLite.R")
biocLite("cn.mops")

cn.mops

cn.mops - Mixture of Poissons for CNV detection in NGS data

Bioconductor version: 2.13

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.

Author: Guenter Klambauer

Maintainer: Guenter Klambauer <cn.mops at bioinf.jku.at>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("cn.mops")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cn.mops")

 

PDF	R Script	cn.mops: Manual for the R package
PDF		Reference Manual

Details

biocViews	Bioinformatics, CellBiology, CopyNumberVariants, Genetics, HapMap, HighThroughputSequencing, HighTroughputSequencingData, Homo_sapiens, Sequencing, Software
Version	1.8.9
In Bioconductor since	BioC 2.9 (R-2.14)
License	LGPL (>= 2.0)
Depends	R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges
Imports	methods, graphics, BiocGenerics, IRanges, Rsamtools
Suggests	snow, DNAcopy
System Requirements
URL	http://www.bioinf.jku.at/software/cnmops/cnmops.html
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	cn.mops_1.8.9.tar.gz
Windows Binary	cn.mops_1.8.9.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	cn.mops_1.8.9.tgz
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