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

Bioconductor version: Release (2.11)

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>

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


biocViews Bioinformatics, CopyNumberVariants, HighThroughputSequencing, Sequencing, Software
Version 1.4.12
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
Depends On Me
Imports Me
Suggests Me

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Package Source cn.mops_1.4.12.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) cn.mops_1.4.12.tgz
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