recipe bioconductor-genomicozone

Delineate outstanding genomic zones of differential gene activity

Homepage

https://bioconductor.org/packages/3.13/bioc/html/GenomicOZone.html

License

LGPL (>=3)

Recipe

/bioconductor-genomicozone/meta.yaml

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.

package bioconductor-genomicozone

Versions

1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-biomart >=2.48.0,<2.49.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-ggbio >=1.40.0,<1.41.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• r-base >=4.1,<4.2.0a0

• r-ckmeans.1d.dp >=4.3.0

• r-ggplot2

• r-gridextra

• r-lsr

• r-plyr

• r-rdpack

Required By

Installation

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

conda install bioconductor-genomicozone

and update with:

conda update bioconductor-genomicozone

or use the docker container:

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

(see bioconductor-genomicozone/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-genomicozone/README.html)