recipe bioconductor-bobafit

Refitting diploid region profiles using a clustering procedure

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/BOBaFIT.html

License:

GPL (>= 3)

Recipe:

/bioconductor-bobafit/meta.yaml

This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

package bioconductor-bobafit

Versions:

1.2.0-0

Depends:

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-ggbio >=1.46.0,<1.47.0

• bioconductor-plyranges >=1.18.0,<1.19.0

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-ggforce

• r-ggplot2

• r-magrittr

• r-nbclust

• r-stringr

• r-tidyr

Required By:

Installation

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

conda install bioconductor-bobafit

and update with:

conda update bioconductor-bobafit

or use the docker container:

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

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

Download stats

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-bobafit/README.html)