RandomWalkRestartMH
A package to perform Random Walk with Restart on different types of networks
Science Score: 13.0%
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Low similarity (12.6%) to scientific vocabulary
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Repository
A package to perform Random Walk with Restart on different types of networks
Basic Info
- Host: GitHub
- Owner: alberto-valdeolivas
- Language: R
- Default Branch: master
- Homepage: https://alberto-valdeolivas.github.io/RandomWalkRestartMH/
- Size: 10.3 MB
Statistics
- Stars: 21
- Watchers: 1
- Forks: 11
- Open Issues: 2
- Releases: 0
Topics
Metadata Files
README.md
RandomWalkRestartMH: An R package to perform Random Walk with Restart
Overview
Random Walk with Restart (RWR) is an algorithm developed to provide the distance
(or closennes) between nodes in a graph. To do so, RWR simulates an imaginary
particle that starts on a seed(s) node(s) and follows randomly the edges of a
network. At each step, there is a restart probability, r, meaning that the
particle can come back to the seed(s).
This package provides an easy interface to apply RWR on different types of complex networks:
A monoplex or single network, which contains solely nodes of the same nature. In addition, all the edges belong to the same category.
A multiplex network, defined as a collection of monoplex networks considered as layers of the multiplex network. In a multiplex network, the different layers share the same set of nodes, but the edges represent relationships of different nature. In this case, the RWR particle can jump from one node to its counterparts on different layers.
A heterogeneous network, which is composed of two monoplex networks containing nodes of different nature. These different kind of nodes can be connected thanks to bipartite edges, allowing the RWR particle to jump between the two networks.
A multiplex and heterogeneous network, which is built by linking the nodes in every layer of a multiplex network to nodes of different nature thanks to bipartite edges.
A full multiplex and heterogeneous network, in which the two networks connected by bipartite interactions are of multiplex nature. The RWR particle can now explore the full multiplex-heterogeneous network.
The user can integrate single networks (monoplex networks) to create a multiplex network. The multiplex network can also be integrated, thanks to bipartite relationships, with another multiplex network containing nodes of different nature. Proceeding this way, a network both multiplex and heterogeneous will be generated.
This package was developed in the context of the following publication:
A Valdeolivas, L Tichit, C Navarro, S Perrin, G Odelin, N Levy, P Cau, E Remy, and A Baudot. 2018. “Random walk with restart on multiplex and heterogeneous biological networks.” Bioinformatics 35 (3). DOI: https://doi.org/10.1093/bioinformatics/bty637
Getting Started
RandomWalkRestartMH is available in Bioconductor.
However, we suggest to use devtools to install the latests version from
this Github repository with the following command.
```r
To install the development version from the Github repo:
install.packages("devtools")
devtools::install_github("alberto-valdeolivas/RandomWalkRestartMH") ```
Then, we strongly suggest to visit the package website and explore the vignette for a proper usage:
Citing RandomWalkRestartMH
Please, cite the following publication if you use our package:
A Valdeolivas, L Tichit, C Navarro, S Perrin, G Odelin, N Levy, P Cau, E Remy, and A Baudot. 2018. “Random walk with restart on multiplex and heterogeneous biological networks.” Bioinformatics 35 (3)
Additional Considerations
Please note that this version of the package does not deal with directed networks. New features will be included in future updated versions of RandomWalkRestartMH.
Owner
- Name: Alberto Valdeolivas
- Login: alberto-valdeolivas
- Kind: user
- Location: Heidelberg, Germany
- Repositories: 2
- Profile: https://github.com/alberto-valdeolivas
Postdoc at Saez Lab
GitHub Events
Total
- Issues event: 1
- Watch event: 3
Last Year
- Issues event: 1
- Watch event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alberto Valdeolivas | a****s@g****m | 114 |
| Nitesh Turaga | n****a@g****m | 10 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| LiNk-NY | m****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 5
- Total pull requests: 6
- Average time to close issues: 9 months
- Average time to close pull requests: less than a minute
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 2.6
- Average comments per pull request: 0.33
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dkainer (3)
- penaloza-7 (1)
- scicrow (1)
- jihunni (1)
Pull Request Authors
- alberto-valdeolivas (5)
- TimBMK (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 10,706 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: RandomWalkRestartMH
Random walk with restart on multiplex and heterogeneous Networks
- Homepage: https://github.com/alberto-valdeolivas/RandomWalkRestartMH
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/RandomWalkRestartMH/inst/doc/RandomWalkRestartMH.pdf
- License: GPL (>= 2)
- Status: removed
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Latest release: 1.26.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- Matrix * imports
- dnet * imports
- igraph * imports
- methods * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests