recipe bioconductor-panviz

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-panviz/meta.yaml

This pacakge integrates data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with summary-level genome-wide association (GWAS) data, such as that provided by the GWAS Catalog or GWAS Central databases, or a user's own study or dataset, in order to produce biological networks, termed IMONs (Integrated Multi-Omic Networks). IMONs can be used to analyse trait-specific polymorphic data within the context of biochemical and metabolic reaction networks, providing greater biological interpretability for GWAS data.

package bioconductor-panviz

(downloads) docker_bioconductor-panviz

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-colorspace:

depends r-data.table:

depends r-dplyr:

depends r-easycsv:

depends r-futile.logger:

depends r-igraph:

depends r-magrittr:

depends r-rcolorbrewer:

depends r-rentrez:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-panviz

and update with::

   mamba update bioconductor-panviz

To create a new environment, run:

mamba create --name myenvname bioconductor-panviz

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-panviz:<tag>

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