DeDaL is a Cytoscape 3.0 app which uses several algorithms of dimention reduction to produce data-driven network layouts based on multidimensional data (typicaly gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another by rotating and mirroring. Combining these possibilities facilitates creating insightful network layouts representing both structural network features and the correlation patterns in multivariate data. The app is implemented in Java. DeDaL app has the following functions:
1. pre-processing options:
* double center data
* network-smooth data
2. Data-Driven Layout:
* Principal Component Analysis (PCA)
* Elastic map (non linear PCA)
* save processed data
3. Layout aligning
4. Layout morphing
DeDaL can be used entirely in Cytoscape or in a command line mode or in a combination of both.
We propose you to follow our [http://bioinfo-out.curie.fr/projects/dedal/#tutorial Tutorial] to see an example of using DeDaL with expression data for two cancer subtypes on Fanconi DNA repair pathway.
