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https://github.com/JoWatson2011/phosphoRWHN
Random Walk on Heterogeneous Network For Functional Analysis of Phosphoproteomics Data
https://github.com/JoWatson2011/phosphoRWHN
Last synced: 1 day ago
JSON representation
Random Walk on Heterogeneous Network For Functional Analysis of Phosphoproteomics Data
- Host: GitHub
- URL: https://github.com/JoWatson2011/phosphoRWHN
- Owner: JoWatson2011
- License: other
- Created: 2021-04-16T16:06:30.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2022-01-24T10:33:15.000Z (almost 3 years ago)
- Last Synced: 2024-08-02T13:31:41.536Z (3 months ago)
- Language: R
- Homepage:
- Size: 21.7 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-proteomics - phosphoRWHN - R - pathway enrichment for phosphoproteomics data - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00150) (7. Protein Pathway Enrichment / Table of Contents)
README
# RWHN_Phosphoproteomics
A method to infer the function of individual phosphorylation sites based on phosphoproteomics data, using random walks on heterogeneous networks (RWHN).
# To install package
Run the following in an R session:
`devtools::install_github("JoWatson2011/phosphoRWHN", build_vignettes = T)`
The [Bioconductor](https://www.Bioconductor.org) packages `org.Hs.eg.db`, `GOSemSim`, `GO.db`, `AnnotationDbi` are also required and may need installing separately.
# To view vignette
Run the following in an R session:
```
library(phosphoRWHN)
vignette("phosphoRWHN_MAPKERK")
```
Manuscript can be viewed [here](https://doi.org/10.1021/acs.jproteome.1c00150):
Watson, Joanne, Jean-Marc Schwartz, and Chiara Francavilla.
“Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites.”
Journal of Proteome Research 20, no. 7 (July 2, 2021): 3532–48. https://doi.org/10.1021/acs.jproteome.1c00150.