| Network inference | Reference | Wrapper function |
|---|
| ARACNE | Margolin, Adam A., et al. "ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context." BMC bioinformatics7.Suppl 1 (2006): S7. | aracne.wrap | | C3NET | Altay, Gökmen, and Frank Emmert-Streib. "Inferring the conservative causal core of gene regulatory networks." BMC Systems Biology 4.1 (2010): 132. | c3net.wrap | | CLR | Faith, Jeremiah J., et al. "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles." PLoS biology 5.1 (2007): e8. | clr.wrap | | GeneNet | Opgen-Rhein, Rainer, and Korbinian Strimmer. "From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data." BMC systems biology 1.1 (2007): 37. | genenet.wrap | | Genie3 | Irrthum, Alexandre, Louis Wehenkel, and Pierre Geurts. "Inferring regulatory networks from expression data using tree-based methods." PloS one 5.9 (2010): e12776. | genie3.wrap | | MutRank | Obayashi, Takeshi, and Kengo Kinoshita. "Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression." DNA research 16.5 (2009): 249-260. | mutrank.wrap | | MRNET | Meyer, Patrick E., et al. "Information-theoretic inference of large transcriptional regulatory networks." EURASIP journal on bioinformatics and systems biology2007 (2007). | mrnet.wrap | | MRNETB | Meyer, Patrick, et al. "Information-Theoretic Inference of Gene Networks Using Backward Elimination." BIOCOMP. 2010. | mrnetb.wrap | | PCIT | Reverter, Antonio, and Eva KF Chan. "Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks." Bioinformatics 24.21 (2008): 2491-2497. | pcit.wrap | | Zscore | Prill, Robert J., et al. "Towards a rigorous assessment of systems biology models: the DREAM3 challenges." PloS one 5.2 (2010): e9202. | zscore.wrap |
|
|
