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# RandomWalkRestartMH: An R package to perform Random Walk with Restart
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
* 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
* 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](https://doi.org/10.1093/bioinformatics/bty637)
## Getting Started
*RandomWalkRestartMH* is available in [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/RandomWalkRestartMH.html).
However, we suggest to use `devtools` to install the latests version from
this Github repository with the following command.
## To install the development version from the Github repo:
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