# graphsim

> R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

**Wikidata**: [Q120964676](https://www.wikidata.org/wiki/Q120964676)  
**Source**: https://4ort.xyz/entity/graphsim

## Summary
**graphsim** is an R package that simulates gene expression data from biological network structures using the `igraph` and `mvtnorm` libraries. It is freely available on CRAN and published in the Journal of Open Source Software (JOSS), making it accessible for researchers in systems biology and computational genetics.

## Key Facts
- **Software type**: Free software (open-source)
- **Latest stable version**: 1.0.4 (released on 2025-05-12)
- **Primary function**: Simulates gene expression data from `igraph` network structures
- **Dependencies**: Uses `mvtnorm` for multivariate normal distribution modeling
- **Hosted on**: GitHub (repository: [TomKellyGenetics/graphsim](https://github.com/TomKellyGenetics/graphsim))
- **Published in**: Journal of Open Source Software (JOSS)
- **Available on**: Comprehensive R Archive Network (CRAN)
- **First release**: Version 0.1.2 (2020-03-16)
- **Described as**: "An R package for simulating gene expression data from graph structures of biological pathways"

## FAQs
### Q: What is graphsim used for?
A: graphsim is used to simulate gene expression data from biological network structures, particularly for researchers studying systems biology and computational genetics. It leverages `igraph` for network modeling and `mvtnorm` for statistical simulations.

### Q: Where can I download graphsim?
A: The latest versions of graphsim are available for download from its GitHub releases page: [https://github.com/TomKellyGenetics/graphsim/releases](https://github.com/TomKellyGenetics/graphsim/releases).

### Q: Is graphsim open-source?
A: Yes, graphsim is free software distributed under open-source terms, allowing users to freely run, study, modify, and distribute it.

### Q: What are the key dependencies of graphsim?
A: graphsim relies on the `igraph` package for network structure representation and the `mvtnorm` package for multivariate normal distribution simulations.

### Q: Has graphsim been published in a peer-reviewed journal?
A: Yes, graphsim has been published in the Journal of Open Source Software (JOSS), ensuring its scientific credibility and accessibility.

## Why It Matters
graphsim addresses a critical need in computational biology by providing a tool for simulating gene expression data from network structures. This capability is essential for testing hypotheses, validating models, and understanding the interplay between genes and biological pathways. By integrating with widely used R packages like `igraph` and `mvtnorm`, graphsim offers a flexible and reproducible framework for researchers. Its open-source nature ensures broad adoption and continuous improvement, making it a valuable resource for the systems biology community.

## Notable For
- **First release**: Version 0.1.2 (March 16, 2020), marking the initial public availability of the package.
- **Latest stable version**: 1.0.4 (May 12, 2025), indicating ongoing maintenance and updates.
- **Published in JOSS**: Ensures the package meets open-source software standards and is peer-reviewed.
- **CRAN availability**: Available on the Comprehensive R Archive Network, making it easily accessible to R users.
- **GitHub repository**: Hosted on GitHub, facilitating community contributions and issue tracking.

## Body
### Overview
graphsim is an R package designed to simulate gene expression data from biological network structures. It utilizes the `igraph` package for network representation and the `mvtnorm` package for multivariate normal distribution modeling, making it a specialized tool for systems biology research.

### Development and Releases
The package was first released as version 0.1.2 on March 16, 2020. Subsequent updates followed, with version 1.0.4 being the latest stable release as of May 12, 2025. Each release is documented on the GitHub repository, providing transparency and accessibility to users.

### Availability and Accessibility
graphsim is freely available on CRAN and published in JOSS, ensuring its scientific credibility and open-source nature. The source code is hosted on GitHub, allowing for community contributions and issue tracking.

### Technical Details
The package simulates gene expression data by modeling interactions within biological networks. It depends on `igraph` for network structure and `mvtnorm` for statistical simulations, making it a robust tool for computational biology applications.

## References

1. [Release 0.1.2. 2020](https://github.com/TomKellyGenetics/graphsim/releases/tag/0.1.2)
2. [Release 1.0.0. 2020](https://github.com/TomKellyGenetics/graphsim/releases/tag/v1.0.0)
3. [Release 1.0.1. 2020](https://github.com/TomKellyGenetics/graphsim/releases/tag/v1.0.1)
4. [Release 1.0.2. 2021](https://github.com/TomKellyGenetics/graphsim/releases/tag/v1.0.2)
5. [Release 1.0.3. 2022](https://github.com/TomKellyGenetics/graphsim/releases/tag/1.0.3)
6. [Release 1.0.4. 2025](https://github.com/TomKellyGenetics/graphsim/releases/tag/v1.0.4)