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Copy number estimation by a Mixture Of PoissonS cn.MOPS

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. It 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.

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cn.MOPS classification

cn.MOPS specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU Lesser General Public License version 3.0
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input format:
BAM, read count matrices
Programming languages:
R
Computer skills:
Advanced
Requirements:
BiocGenerics, Biobase, IRanges, GenomicRanges

cn.MOPS distribution

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cn.MOPS support

Documentation

Maintainer

  • Guenter Klambauer <>

Credits

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Publications

Institution(s)

Institute of Bioinformatics, Johannes Kepler University,Linz, Austria

Link to literature

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