synRNASeqNet: Synthetic RNA-Seq Network Generation and Mutual Information Estimates

It implements various estimators of mutual information, such as the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, the shrinkage estimator, and the Chao-Shen estimator. It also offers wrappers to the kNN and kernel density estimators. Furthermore, it provides various index of performance evaluation such as precision, recall, FPR, F-Score, ROC-PR Curves and so on. Lastly, it provides a brand new way of generating synthetic RNA-Seq Network with known dependence structure.

AuthorLuciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Date of publication2015-04-20 11:55:18
MaintainerLuciano Garofano <lucianogarofano88@gmail.com>
LicenseGPL (>= 3)
Version1.0
https://github.com/lucgar/synRNASeqNet

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Files in this package

synRNASeqNet
synRNASeqNet/NAMESPACE
synRNASeqNet/R
synRNASeqNet/R/plotPR.R synRNASeqNet/R/performanceNET.R synRNASeqNet/R/entropyCS.R synRNASeqNet/R/Likelihoods.R synRNASeqNet/R/shrinkageIntensity.R synRNASeqNet/R/entropyShrink.R synRNASeqNet/R/entropyBayes.R synRNASeqNet/R/getTask.R synRNASeqNet/R/entropyMM.R synRNASeqNet/R/parMIEstimate.R synRNASeqNet/R/thetaBayes.R synRNASeqNet/R/parEntropyEstimate.R synRNASeqNet/R/simulatedData.R synRNASeqNet/R/parMIKD.R synRNASeqNet/R/DiscriminantPower.R synRNASeqNet/R/diagId.R synRNASeqNet/R/synRNAseqNet-internal.R synRNASeqNet/R/YoudenIndex.R synRNASeqNet/R/performanceIndex.R synRNASeqNet/R/getIndex.R synRNASeqNet/R/plotROC.R synRNASeqNet/R/startId.R synRNASeqNet/R/entropyML.R synRNASeqNet/R/beta_k.R synRNASeqNet/R/aucDisc.R synRNASeqNet/R/thetaGT.R synRNASeqNet/R/thetaShrink.R synRNASeqNet/R/thetaML.R synRNASeqNet/R/mainNetFunction.R
synRNASeqNet/MD5
synRNASeqNet/DESCRIPTION
synRNASeqNet/man
synRNASeqNet/man/YoudenIndex.Rd synRNASeqNet/man/performanceIndex.Rd synRNASeqNet/man/Likelihoods.Rd synRNASeqNet/man/aucDisc.Rd synRNASeqNet/man/plotPR.Rd synRNASeqNet/man/DiscriminantPower.Rd synRNASeqNet/man/simulatedData.Rd synRNASeqNet/man/parMIKD.Rd synRNASeqNet/man/synRNASeqNet-internal.Rd synRNASeqNet/man/performanceNET.Rd synRNASeqNet/man/entropyMM.Rd synRNASeqNet/man/mainNetFunction.Rd synRNASeqNet/man/plotROC.Rd synRNASeqNet/man/parMIEstimate.Rd synRNASeqNet/man/entropyML.Rd synRNASeqNet/man/entropyCS.Rd synRNASeqNet/man/parEntropyEstimate.Rd synRNASeqNet/man/entropyShrink.Rd synRNASeqNet/man/synRNASeqNet-package.Rd synRNASeqNet/man/entropyBayes.Rd

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