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

View on CRAN

Functions

aucDisc Man page
beta_k Man page
diagId Man page
DiscriminantPower Man page
entropyBayes Man page
entropyCS Man page
entropyML Man page
entropyMM Man page
entropyShrink Man page
getIndex Man page
getTask Man page
Likelihoods Man page
mainNetFunction Man page
parEntropyEstimate Man page
parMIEstimate Man page
parMIKD Man page
performanceIndex Man page
performanceNET Man page
plotPR Man page
plotROC Man page
shrinkageIntensity Man page
simulatedData Man page
startId Man page
synRNASeqNet Man page
synRNASeqNet-package Man page
thetaBayes Man page
thetaGT Man page
thetaML Man page
thetaShrink Man page
YoudenIndex Man page

Files

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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