README.md

In kkmann/pwcuratr: Functional Pathway Cluster Curation tool

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:

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.

kkmann/pwcuratr documentation built on March 7, 2020, 2 a.m.