genewalkR

Description

This package implements various computational biology methods based on graphs:

• More "simple" diffusion algorithms of labels over networks that have been translated into Rust for speed and reduced memory pressure.
• Methods leveraging node2vec, a small graph neural network.

For now, the following methods implemented:

• Various diffusion methods for "guilty-by-association" approaches, see Tsuda et al., Vandin et al., Bersanelli et al. and Mostafavi et al..
• Diffusion profiles from Ruiz et al.: one constrained personalised PageRank per seed over a heterogeneous graph, with sink node types and type weights, then distances between the profiles. See this vignette.
• General node2vec to generate embeddings, please see this vignette.
• metapath2vec (and metapath2vec++), the extension of node2vec to heterogeneous graphs. Walks follow a metapath over node types, e.g. gene-pathway-gene. See this vignette.
• The GeneWalk approach from Ietswaart et al. (see GitHub here). If you want to use this, please check out this vignette.
• A Gene context drift type approach akin to Jassim et al. Specifically the part of running node2vec over two networks, followed by Procruste alignment and identifying node embeddings that differ between the two networks, indicating a context drift for these nodes/genes. Details can be found in this vignette.

Installation

You will need Rust on your system to have the package working. An installation guide is provided here. There is a bunch of further help written here by the rextendr guys in terms of Rust set up. (genewalkR uses rextendr to interface with Rust.)

Setting up the Rust toolchain

Steps for installation:

1. In the terminal, install Rust

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

2. In R, install rextendr:

install.packages("rextendr")

3. Finally install genewalkR:

devtools::install_github("https://github.com/GregorLueg/genewalkR")

Install genewalkR

You can install from R-universe:

install.packages(
  'genewalkR', 
  repos = c('https://gregorlueg.r-universe.dev', 'https://cloud.r-project.org')
)

Or from source which will compile all the Rust.

# From GitHub
remotes::install_github("GregorLueg/genewalkR")

How to use the package

Please refer to the package website. Vignettes and function definitions are provided there. If you run into issues, please use GitHub issues.

Working with an LLM coding agent? install_agent_skill() drops a genewalkR skill into your agent set up so it stops guessing at the API.

Roadmap

While more complex graph neural networks that leverage edge and node information are in vogue at the moment, some simple methods in times tend to do quite well themselves, while not necessitating massive amounts of (GPU) compute. metapath2vec and the diffusion profiles are the first steps in that direction: heterogeneous graphs, still on CPU. A few additional graph-based methods are also already implemented in bixverse, here more with focus on PageRank-based ones and a lot of methods that use kNN graphs in some colour or shape (specifically for single cell).

License

Copyright (c) 2025 genewalkR authors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.