Package Recipe 'bioconductor-sbgnview'

recipe bioconductor-sbgnview

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/SBGNview.html
License:: AGPL-3
Recipe:: /bioconductor-sbgnview/meta.yaml

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¶

Versions:

1.24.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.1-0, 1.4.0-0,

1.24.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.1-0, 1.4.0-0, 1.2.0-0, 1.0.0-1

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-keggrest >=1.50.0,<1.51.0
on bioconductor-pathview >=1.50.0,<1.51.0
on bioconductor-sbgnview.data >=1.24.0,<1.25.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-bookdown
on r-httr
on r-igraph
on r-knitr
on r-rdpack
on r-rmarkdown
on r-rsvg
on r-xml2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-sbgnview

to add into an existing workspace instead, run:

pixi add bioconductor-sbgnview

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-sbgnview

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-sbgnview

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-sbgnview:<tag>

(see bioconductor-sbgnview/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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-sbgnview/README.html)