- recipe bioconductor-bobafit
Refitting diploid region profiles using a clustering procedure
GPL (>= 3)
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¶
- depends bioconductor-genomicranges:
- depends bioconductor-ggbio:
- depends bioconductor-plyranges:
- depends r-base:
- depends r-dplyr:
- depends r-ggforce:
- depends r-ggplot2:
- depends r-magrittr:
- depends r-nbclust:
- depends r-stringr:
- depends r-tidyr:
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
myenvnamebeing 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>``)