- recipe bioconductor-sbgnview
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.
- package bioconductor-sbgnview¶
- depends bioconductor-annotationdbi:
- depends bioconductor-keggrest:
- depends bioconductor-pathview:
- depends bioconductor-sbgnview.data:
- depends bioconductor-summarizedexperiment:
- depends r-base:
- depends r-bookdown:
- depends r-httr:
- depends r-igraph:
- depends r-knitr:
- depends r-rdpack:
- depends r-rmarkdown:
- depends r-rsvg:
- depends r-xml2:
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-sbgnview and update with:: mamba update bioconductor-sbgnview
To create a new environment, run:
mamba create --name myenvname bioconductor-sbgnview
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-sbgnview:<tag> (see `bioconductor-sbgnview/tags`_ for valid values for ``<tag>``)