recipe bioconductor-cn.mops

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/cn.mops.html

License:

LGPL (>= 2.0)

Recipe:

/bioconductor-cn.mops/meta.yaml

Links:

biotools: cn.mops

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++.

package bioconductor-cn.mops

Versions:

1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0, 

1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-1,  1.18.0-0,  1.16.2-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-exomecopy >=1.44.0,<1.45.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

Required By:

• bioconductor-panelcn.mops

• bioconductor-copynumberplots

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-cn.mops

and update with:

conda update bioconductor-cn.mops

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-cn.mops:<tag>

(see bioconductor-cn.mops/tags for valid values for <tag>)

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