Cyni Toolbox

Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
Cytoscape Network Inference Toolbox (**Cyni**) is a new Cytoscape App that puts together several tools that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks. The goal of Cyni is to make network inference more accessible to biologists by providing user-friendly solution as well as provide a framework to bio-informaticiens to develop and apply their new techniques. Data imputation and discretization techniques are provided along with several known inference algorithms to make this tool fully operational for any kind inference requirement. While data imputation and discretization techniques allow you modify Cytoscape tables, network inference algorithms produce a new network after applying the chosen technique. Cyni provides: * Several commonly used network inference techniques * Data imputation and discretization techniques for preprocessing * Documented API Complete user documentation can be found through the **Website** link. In case, it is not working, please use this [https://github.com/schwikowskilab/cyniProject/wiki link]. If you are interested in creating a network inference app through the Cyni framework, all documentation needed is available through the **Tutorial** link.

1.0.0.beta6

Works with Cytoscape 3.1

API   pom.xml   Javadocs

Apps that depend on this release

Release Notes

This release contains several improvements: - First no beta API - New Cyni UI - Fixed several bugs mainly in HC algorithm - Upgraded to support Cytoscape 3.1 functionality such as commands

1.0.0.beta5

Works with Cytoscape 3.0

API   pom.xml   Javadocs

Release Notes

This release contains the following changes: - A new API version (beta2) with several improvements such as a new possibility to provide own UI panel without need to use Cytoscape Tunables - Entropy Metric improved by providing several possible implementations that can be selected through parameters (Web documentation for more info) - Methods K2 and Hill Climbing has been improved to better use log metrics such as MDL or AIC

1.0.0.beta4

Works with Cytoscape 3.0

API   pom.xml   Javadocs

Release Notes

This release contains the following changes: - A new manual discretization tool (UI works better with Cytoscape 3.0.1) - Several Bugs fixed - Several metrics improved - Imputation parameters definition improved

1.0.0.beta3

Works with Cytoscape 3.0

API   pom.xml   Javadocs

Release Notes

This release contains the following changes: - A new mutual information inference algorithm - Correlation Inference algorithm allows using signed or absolute correlation values to infer new networks - Several bugs fixed