Mutual Information Reconstruction Methods: CLR:Context Likelihood or Relatedness Network Reconstruction Algorithm. Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877. ARACNE.M:Reconstruction of Accurate Cellular Networks (Multiplicative Model). Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877. ARACNE.A:Reconstruction of Accurate Cellular Networks (Additive Model). Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877. MRNET.A:Reconstruction using the Maximum Relevance Minimum Redundancy Method. Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877. MRNET.B:Reconstruction using the Maximum Relevance Minimum Redundancy Method (Backward). Meyer, P.E., Lafitte, F., Bontempi, G. (2008) Minet: A r/bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics, 9, art. no. 461. C3NET:Inferred Reconstruction Network using Mutual Information. Altay, G., Emmert-Streib, F. (2011) Structural influence of gene networks on their inference: Analysis of C3NET. Biology Direct, 6, art. no. 31.
Correlation Based Reconstruction Methods: WGCNA:Weighted Correlation Reconstruction Method. Langfelder, P., Horvath, S. (2008) WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics, 9, art. no. 559.
Regression Reconstruction Methods: GeneNet:Reconstruction Method using Gaussian Mixture Models. A. Werhli, M. Grzegorczyk, and D. Husmeier (2006) Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. Bioinformatics, 22, 2523�2531. Zhong R, Allen JD, Xiao G, Xie Y (2014) Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PLoS One, 9, e106319
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