recipe bioconductor-bobafit

Refitting diploid region profiles using a clustering procedure

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-bobafit

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-ggbio:

>=1.50.0,<1.51.0

depends bioconductor-plyranges:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggforce:

depends r-ggplot2:

depends r-magrittr:

depends r-nbclust:

depends r-stringr:

depends r-tidyr:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-bobafit

and update with::

   mamba update bioconductor-bobafit

To create a new environment, run:

mamba create --name myenvname bioconductor-bobafit

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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 install-with-bioconda 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)