A set of functions providing the implementation of the network meta-analysis model with dose-response relationships, predicted values of the fitted model and dose-response plots in a frequentist way.

Social network analysis has become an essential tool in the study of complex systems. 'NetExplorer' allows to visualize and explore complex systems. It is based on 'd3js' library that brings 1) Graphical user interface;  2) Circular, linear, multilayer and force Layout; 3) Network live exploration and 4) SVG exportation.

Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.

The Bayesian hierarchical model named antigen-T cell interaction estimation is to estimate the history of the immune pressure on the evolution of the tumor clones.The model is based on the estimation result from Andrew Roth (2014) <doi:10.1038/nmeth.2883>.

Given a network (e.g. a food web), estimates several network indices. These include: Ascendency network indices, Direct and indirect dependencies, Effective measures, Environ network indices, General network indices, Pathway analysis, Network uncertainty indices and constraint efficiencies and the trophic level and omnivory indices of food webs.

Implementation of network integration approaches
    comprising unweighted and weighted integration methods. Unweighted integration
    is performed considering the average, per-edge average, maximum and minimum of
    networks edges. Weighted integration takes into account a weight for each 
    network during the fusion process, where the weights express
    the ''predictiveness strength'' of each network considering a specific predictive
    task. Weights can be learned using a machine learning algorithm able to associate
    the weights to the assessment of the accuracy of the learning algorithm 
    trained on the network itself. The implemented methods can be applied to 
    effectively integrate different biological networks modelling a wide range
    of problems in bioinformatics (e.g. disease gene prioritization, protein
    function prediction, drug repurposing, clinical outcome prediction).