MCODE Cytoscape App 2.0¶
MCODE is a Cytoscape app that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. Cytoscape is freely available network visualization and analysis software.
MCODE is a relatively fast method of clustering. With an intuitive interface, it is suited for both computationally and biologically oriented researchers. Current features include:
Fast network clustering
Fine-tuning of results with numerous node-scoring and cluster-finding parameters
Interactive cluster boundary and content exploration
Multiple result set management
Cluster sub-network creation and plain text export
Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the MCODE paper for more information.
Feature Requests and Reporting Bugs¶
The MCODE GitHub issue tracker can be used to report a bug or request a feature.
To Report a bug:
Click on New Issue
Write a short description of the issue. It is very helpful to provide a series of steps that can be taken to reproduce the issue.
If possible attach a session file (.cys) or example input files.
Enter App version, Cytoscape version and operating system.
Click on Submit new issue
- Running MCODE
- The User Interface
- Getting and Interpreting Results
- Fine-Tuning Your Analysis
- Exploring Results Interactively
- Outputting Results