SQUADD-package
(Package: SQUADD) :
Collection of visualization tools to perform a SQUAD-based quantitative analysis
The SQUAD (Standardized Qualitative Dynamical Systems) software is dedicated to the analysis of boolean logical model(Di Cara et al 2007). It was the first tool to combine the traditional boolean approach and a continuous system. This novel feature permits the dynamical analysis of regulatory network in the absence of kinetic data. In order to get the best of this approach, we provide here a R package, SQUADD, a SQUAD add-on for : (i) simplify the visualization of the initial SQUAD simulation results. (ii) generate qualitative predictions of the component change between two conditions. (iii) Assess the coherence of a model by PCA analysis.
This method creates a table containing the interpolated/fitted value of the simulation curve at the user-defined time point. Each column represents the condition and each line, the component node. It is used as basis for the Correlation Circle and the Prediction Map.
This method creates a table containing the interpolated/fitted value of the simulation curve at the user-defined time point. Each column represents the condition and each line, the component node. It is used as basis for the Correlation Circle and the Prediction Map.
This method generates the correlation circle. Correlation circle is used to assess the coherence of a model. Indeed, each vector represents our conditions and the angle between each vector give the correlation between the variables. if the angle is higher than 90 degree there is no correlation.
plotCC
(Package: SQUADD) :
Generate the Correlation Circle.
This method generates the correlation circle. Correlation circle is used to assess the coherence of a model. Indeed, Each vector represents our conditions and the angle between each vector give the correlation between the variables. if the angle is higher than 90 degrees there is no correlation.
This method is used to create a simulation matrix. A simulation matrix permits to follow the activation signal of an user-defined number of Node. Each columns correspond to the user-selected component node and the each rows, to the conditions. (more details in plotSimMatrix)
providing 
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