CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data
Christopher A. Penfold, Ahmed Shifaz, Paul E. Brown, Ann E. Nicholson, David L. Wild · Statistical Applications in Genetics and Molecular Biology · 2015
Here we introduce the causal structure identification (CSI) package, a Gaussian process based approach to inferring gene regulatory networks (GRNs) from multiple time series data. The standard CSI approach infers a single GRN via joint learning from multiple time series datasets; the hierarchical approach (HCSI) infers a separate GRN for each dataset, albeit with the networks constrained to favor similar structures, allowing for the identification of context specific networks. The software is implemented in MATLAB and includes a graphical user interface (GUI) for user friendly inference. Finally the GUI can be connected to high performance computer clusters to facilitate analysis of large genomic datasets.