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genewalkR package

r_packageCI License: MIT pkgdown

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Description

This package implements various computational biology methods that use node2vec under the hood. It leverages the rextendr interface into Rust to make these methods VERY fast. For now, we have the following methods implemented:

  • General node2vec to generate embeddings, please 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 around running node2vec onto two networks, followed by Procruste alignment and identifying node embeddings that differ between the two networks. 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
  1. In R, install rextendr:
install.packages("rextendr")
  1. Finally install genewalkR:
devtools::install_github("https://github.com/GregorLueg/genewalkR")

Install genewalkR 

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

How to use the package

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

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.