recipe bioconductor-exomecopy

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/exomeCopy.html

License

GPL (>= 2)

Recipe

/bioconductor-exomecopy/meta.yaml

Links

biotools: exomecopy, doi: 10.2202/1544-6115.1732

package bioconductor-exomecopy

(downloads) docker_bioconductor-exomecopy

Versions

1.28.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends libgcc-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-exomecopy

and update with:

conda update bioconductor-exomecopy

or use the docker container:

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

(see bioconductor-exomecopy/tags for valid values for <tag>)