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/.
