cn.mops
This package is for version 3.18 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: 3.18
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("cn.mops")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual |
Details
| biocViews | CellBiology, CopyNumberVariation, Genetics, HapMap, Homo_sapiens, Sequencing, Software |
| Version | 1.48.0 |
| 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, exomeCopy |
| 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 | CNVgears |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cn.mops_1.48.0.tar.gz |
| Windows Binary | cn.mops_1.48.0.zip |
| macOS Binary (x86_64) | cn.mops_1.48.0.tgz |
| macOS Binary (arm64) | cn.mops_1.48.0.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 |