https://github.com/kkmann/pwcuratr
Curate gene pathway clusters using functional interactions
https://github.com/kkmann/pwcuratr
curation pathways reactome
Last synced: about 2 months ago
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Curate gene pathway clusters using functional interactions
- Host: GitHub
- URL: https://github.com/kkmann/pwcuratr
- Owner: kkmann
- License: other
- Created: 2020-02-25T16:47:00.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-03-06T00:53:04.000Z (about 5 years ago)
- Last Synced: 2025-04-02T04:42:55.827Z (about 2 months ago)
- Topics: curation, pathways, reactome
- Language: R
- Homepage: https://kkmann.github.io/pwcuratr/
- Size: 68.7 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://zenodo.org/badge/latestdoi/243048629)
[](https://travis-ci.com/kkmann/pwcuratr)
[](https://codecov.io/gh/kkmann/pwcuratr?branch=master)
[](https://mybinder.org/v2/gh/kkmann/pwcuratr/master?urlpath=shiny/inst/shiny/)
# 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
```{r}
remotes::install_github("kkmann/pwcuratr")
```
Tagged releases are available via, e.g.,
```{r}
remotes::install_github("kkmann/[email protected]")
```
## 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
```{r}
pwcuratr::start_shiny_app()
```
or online via mybinder.org.
Links to the most current development version or older tagged releases are
available:
[](https://mybinder.org/v2/gh/kkmann/pwcuratr/master?urlpath=shiny/inst/shiny/)
[](https://mybinder.org/v2/gh/kkmann/pwcuratr/0.2.1?urlpath=shiny/inst/shiny/)
[](https://mybinder.org/v2/gh/kkmann/pwcuratr/0.2.2?urlpath=shiny/inst/shiny/)
## 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.