cn.mops

DOI:10.18129 / B9.bioc.cn.mops

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

Bioconductor版本:发行版(3.13)

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++.

作者:Guenter Klambauer

维护者:Gundula Povysil < Povysil at bioinf.jku.at>

安装

要安装此包，请启动R(版本“4.1”)并输入:

如果(!requireNamespace("BiocManager"， quiet = TRUE)) install.packages("BiocManager")

对于R的旧版本，请参考相应的Bioconductor释放．

文档

要查看系统中安装的此包版本的文档，请启动R并输入:

browseVignettes(“cn.mops”)

PDF	R脚本	cn.mops: Manual for the R package
PDF		参考手册

细节

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版本	1.38.0
在Bioconductor	BioC 2.9 (R-2.14)(9.5年)
许可证	LGPL (>= 2.0)
取决于	R(>= 2.12)，方法，utils，统计，图形，并行，GenomicRanges
进口	BiocGenerics，Biobase，IRanges，Rsamtools，GenomeInfoDb，S4Vectors，exomeCopy
链接
建议	DNAcopy
SystemRequirements
增强了
URL	http://www.bioinf.jku.at/software/cnmops/cnmops.html
全靠我	panelcn.mops
进口我	CopyNumberPlots
建议我	CNVgears
链接到我
构建报告

包档案

遵循bob 体育网址 在R会话中使用此包的说明。

源包	cn.mops_1.38.0.tar.gz
Windows二进制	cn.mops_1.38.0.zip
macOS 10.13 (High Sierra)	cn.mops_1.38.0.tgz
源库	Git克隆https://git.bioconductor.org/packages/cn.mops
源存储库(开发人员访问)	Git克隆git@git.bioconductor.org:packages/cn.mops
包短Url	//www.anjoumacpherson.com/packages/cn.mops/
软件包下载报告	下载数据