recipe bioconductor-cnviz

Copy Number Visualization

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/CNViz.html

License:

Artistic-2.0

Recipe:

/bioconductor-cnviz/meta.yaml

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

package bioconductor-cnviz

(downloads) docker_bioconductor-cnviz

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-copynumberplots:

>=1.18.0,<1.19.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-karyoploter:

>=1.28.0,<1.29.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-dt:

depends r-magrittr:

depends r-plotly:

depends r-scales:

depends r-shiny:

>=1.5.0

requirements:

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-cnviz

and update with::

   mamba update bioconductor-cnviz

To create a new environment, run:

mamba create --name myenvname bioconductor-cnviz

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-cnviz:<tag>

(see `bioconductor-cnviz/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-cnviz/README.html)