cn.mops

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cn.mops.

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

Bioconductor version: 3.12

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

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

Installation

To install this package, start R (version "4.0") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, CopyNumberVariation, Genetics, HapMap, Homo_sapiens, Sequencing, Software
Version	1.36.0
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 years)
License	LGPL (>= 2.0)
Depends	R (>= 2.12), methods, utils, stats, graphics, parallel, GenomicRanges
Imports	BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors, exomeCopy
System Requirements
URL	http://www.bioinf.jku.at/software/cnmops/cnmops.html

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_1.36.0.tar.gz
Windows Binary	cn.mops_1.36.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	cn.mops_1.36.0.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
Old Source Packages for BioC 3.12	Source Archive