The MCODE plugin for Cytoscape provides a user-friendly interface for users to detect molecular complexes in PPI networks. The plugin enables users to easily integrate MCODE into their Cytoscape workflow, facilitating the detection and analysis of molecular complexes. The plugin is expected to be useful for researchers and analysts who want to study molecular complexes in PPI networks.
A typical story: A researcher builds a yeast or human PPI network (e.g., from BioGRID or STRING). They run MCODE and see clusters like: mcode cytoscape
: Every node is assigned a weight based on its local neighborhood density. This weight reflects how many of its neighbors are also connected to each other. The MCODE plugin for Cytoscape provides a user-friendly
$$ \begin{aligned} &x \in \mathbb{R} \ &\text{ PPI network} \ & G = (V,E) \end{aligned} $$ A typical story: A researcher builds a yeast