Skip to content

kkmann/pwcuratr

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

53 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

DOI Travis build status Codecov test coverage badge

Curate gene pathway clusters using functional gene-gene interactions

This package is intended to facilitate candidate gene analyses by allowing the curation of functional 'neighborhoods' for a list of initial genes ('seed genes'). A reactome.org snapshot can be queried for biological pathways that contain any of the seed genes. After selecting a list of interesting reactome.org pathways, the set of all genes participating in these pathways can be pruned by the edge-distance in the graph defined by a set of predicted functional gene-gene interactions [1].

Installation

The most current developments version can be installed via

remotes::install_github("kkmann/pwcuratr")

Tagged releases are available via, e.g.,

remotes::install_github("kkmann/pwcuratr@0.2.1")

Shiny app

To facilitate interactive pathway cluster curation, a shiny app is distributed together with the package. The shiny app can be run locally via

pwcuratr::start_shiny_app()

or online via mybinder.org. Links to the most current development version or older tagged releases are available:

badge badge badge

Documentation

The documentation of the package itself is hosted at https://kkmann.github.io/pwcuratr/.

References

[1]: Wu, G., Feng, X., & Stein, L. (2010). A human functional protein interaction network and its application to cancer data analysis. Genome biology, 11(5), R53.

About

Curate gene pathway clusters using functional interactions

Topics

Resources

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md

Stars

Watchers

Forks

Languages