Software Downloads
Causal Structure Identification (Chris Penfold, Paul Brown, Ahmed Shifaz, Ann Nicholson & David Wild)
A MATLAB implementation of the causal structure identification (CSI) and hierarchical causal structure identification (HCSI) algorithms for inferring gene regulatory networks. The package includes a graphical front end and the ability to visualise results and export networks to Cytoscape.
Requirements: MATLAB (Toolboxes: gpml)
| See | Penfold et al, (2015). CSI: A Nonparametric Bayesian Approach to Network Inference from Multiple Perturbed Time Series Gene Expression Data. Statistical Applications in Genetics and Molecular Biology. In press |
| Penfold & Wild, (2011). How to infer gene networks from expression profiles, revisited. Interface Focus 1 857-870. doi:10.1098/rsfs.2011.0053 | |
| Penfold et al., (2012). Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. Bioinformatics 28(12) i233-i241 doi:10.1093/bioinformatics/bts222 |