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cn.mops

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


Bioconductor version: Release (3.19)

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 [aut], Gundula Povysil [cre]

Maintainer: Gundula Povysil <povysil at bioinf.jku.at>

Citation (from within R, enter citation("cn.mops")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cn.mops")

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

Details

biocViews CellBiology, CopyNumberVariation, Genetics, HapMap, Homo_sapiens, Sequencing, Software
Version 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License LGPL (>= 2.0)
Depends R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges
Imports BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors
System Requirements
URL http://www.bioinf.jku.at/software/cnmops/cnmops.html
See More
Suggests DNAcopy
Linking To
Enhances
Depends On Me panelcn.mops
Imports Me CopyNumberPlots
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cn.mops_1.50.0.tar.gz
Windows Binary cn.mops_1.50.0.zip
macOS Binary (x86_64) cn.mops_1.50.0.tgz
macOS Binary (arm64) cn.mops_1.50.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cn.mops
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cn.mops
Bioc Package Browser https://code.bioconductor.org/browse/cn.mops/
Package Short Url https://bioconductor.org/packages/cn.mops/
Package Downloads Report Download Stats