RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer "dual regulons", a new concept that tests whether regulon pairs agree on the predicted downstream effects.
|Depends:||R (>= 3.4.0), methods, RTN|
|Imports:||grDevices, stats, utils|
|Suggests:||knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics|
|biocViews:||NetworkInference, NetworkEnrichment, GeneRegulation, GeneExpression, GraphAndNetwork|
|MBR-class:||an S4 class for co-regulation analysis and inference of 'dual regulons'.|
|mbrPreprocess:||a preprocessing function for objects of class MBR.|
|mbrPermutation:||inference of transcriptional networks.|
|mbrBootstrap:||inference of consensus transcriptional networks.|
|mbrDpiFilter:||a filter based on the Data Processing Inequality (DPI) algorithm.|
|mbrAssociation:||motifs analysis and inference of "dual regulons".|
|mbrDuals:||a summary for results from the MBR methods.|
|tni2mbrPreprocess:||a preprocessing function for objects of class MBR.|
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Vinicius S. Chagas, Clarice S. Groeneveld, Kerstin B Meyer, Gordon Robertson, Mauro A. A. Castro
Fletcher M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Nature Communications, 4:2464, 2013.
Castro M.A.A. et al., Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48:12-21, 2016.
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