Overview
Graphia imports graphs or builds correlation networks from numerical tables, with clustering and interactive 2D or 3D views. It is a general visual-analysis environment included here for downstream MS metabolomics, rather than a mass-spectrometry processing engine.
What can this tool do?
Common uses
- Explore feature-correlation networks after preprocessing.
- Cluster and compare annotated graph components.
Scientific fit
Primary function
Visualization and reporting
Data compatibility
Inputs
Feature or peak table, Statistical results, Pathway or reaction data
Outputs
Human-readable report
Input formats
CSV numeric tables or GraphML graphs
Output formats
Interactive network views and exported analysis results
Scope and considerations
Designed for
- General graph analysis and visual exploration of numerical-data relationships.
Not designed for
- MS/MS matching, raw-data processing or inference of causal biochemical interactions.
Important requirements
- A cleaned numerical matrix or an existing graph with meaningful identifiers.
Considerations
- Normalization, missing values, batch effects and correlation thresholds influence network structure.
- Graph clusters are exploratory patterns and need independent biological assessment.
Access and documentation
Open-source desktop software with Windows, macOS and Linux downloads. The official site also offers a browser version; assess its suitability separately for your data and deployment requirements.
License: GPL-3.0
Evidence and review
Official project documentation and direct tool publications reviewed on 2026-09-12. Included for downstream MS metabolomics. No installation, dataset analysis or independent performance benchmarking performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Freeman TC, et al. Graphia: A platform for the graph-based visualisation and analysis of high dimensional data. PLOS Computational Biology 18, e1010310 (2022). doi:10.1371/journal.pcbi.1010310
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · First committed entry
Add network visualization specialists and curated relationships
View change · Entry at this revision