- recipe bioconductor-pathview
a tool set for pathway based data integration and visualization
Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
- package bioconductor-pathview¶
- depends bioconductor-annotationdbi:
- depends bioconductor-graph:
- depends bioconductor-kegggraph:
- depends bioconductor-keggrest:
- depends bioconductor-org.hs.eg.db:
- depends bioconductor-rgraphviz:
- depends r-base:
- depends r-png:
- depends r-xml:
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-pathview and update with:: mamba update bioconductor-pathview
To create a new environment, run:
mamba create --name myenvname bioconductor-pathview
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-pathview:<tag> (see `bioconductor-pathview/tags`_ for valid values for ``<tag>``)