recipe bioconductor-copywriter

Copy number information from targeted sequencing using off-target reads

Homepage

https://bioconductor.org/packages/3.11/bioc/html/CopywriteR.html

License

GPL-2

Recipe

/bioconductor-copywriter/meta.yaml

Links

biotools: copywriter, doi: 10.1186/s13059-015-0617-1

CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

package bioconductor-copywriter

Versions

2.20.0-0,  2.18.0-1,  2.16.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0

Depends

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-chipseq >=1.38.0,<1.39.0

• bioconductor-copyhelper >=1.20.0,<1.21.0

• bioconductor-dnacopy >=1.62.0,<1.63.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-futile.logger

• r-gtools

• r-matrixstats

Required By

Installation

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

conda install bioconductor-copywriter

and update with:

conda update bioconductor-copywriter

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-copywriter/README.html)