recipe bioconductor-sbgnview

Overlay omics data onto SBGN pathway diagram

Homepage

https://bioconductor.org/packages/3.12/bioc/html/SBGNview.html

License

AGPL-3

Recipe

/bioconductor-sbgnview/meta.yaml

SBGNview is an R package for visualizing omics data on SBGN pathway maps. Given omics data and a SBGN-ML file with layout information, SBGNview can display omics data as colors on glyphs and output image files. SBGNview provides extensive options to control glyph and edge features (e.g. color, line width etc.). To facilitate pathway based analysis, SBGNview also provides functions to extract molecule sets from SBGN-ML files. SBGNview can map a large collection of gene, protein and compound ID typs to glyphs.

package bioconductor-sbgnview

Versions

1.4.0-0,  1.2.0-0,  1.0.0-1

Depends

• bioconductor-annotationdbi >=1.52.0,<1.53.0

• bioconductor-pathview >=1.30.0,<1.31.0

• bioconductor-sbgnview.data >=1.4.0,<1.5.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• r-base >=4.0,<4.1.0a0

• r-igraph

• r-knitr

• r-rdpack

• r-rmarkdown

• r-rsvg

• r-xml2

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-sbgnview

and update with:

conda update bioconductor-sbgnview

or use the docker container:

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

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

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)