| canonicalModel_ | Decifer a 'model parameter' and run appropriate 'glm_...'... |
| Combine | This is data is the mRNA expression across samples and miRNA... |
| combiner | combiner combines the miRNA and mRNA files |
| corMirnaRna | corMirnaRna correlation for miRNA and mRNA |
| corMirnaRnaMiranda | corMirnaRnaMiranda correlation for miRNA and mRNA |
| corr_0 | This is data is the mRNA FC and miRNA FC correlation data.... |
| downloadMirandaFile | downloadMirandaFile Read internal Miranda file |
| drawCorPlot | drawCorPlot correlation plots for mRNA and miRNA regression... |
| drawInterPlots | drawInterPlots for finInterResult miRNA and mRNA... |
| fdrSig | fdrSig Ruturns FDR significant miRNA/mRNA predictions |
| final_results | This is data is the mRNA FC and miRNA FC... |
| finInterResult | finInterResult miRNA and mRNA interrelation in two-time... |
| geneVari | geneVari Makes a list of gene names to be used in the... |
| geneVariant | This is data is the mRNA expression across samples and miRNA... |
| getInputSpecies | Return Miranda data for a given species. |
| glm_gaussian | Model functions for GLM with Gaussian model. |
| glm_multi | Model functions for GLM with negative binomial family. |
| glm_nb | Model functions for GLM with negative binomial family. |
| glm_poisson | Model functions for GLM with Poisson model. |
| glm_zeroinfl | Model functions for zero inflated model using either Poisson... |
| glm_zeroinfl_negbin | alias for glm_zeroinfl("negbin") |
| glm_zeroinfl_poisson | alias for glm_zeroinfl("poisson") |
| importMirandaFile | importMirandaFile Read internal Miranda file |
| inter0 | This is data is the mRNA FC and miRNA FC... |
| makeFormulaRightSide | makeFormulaRightSide makes right hand side of formula for... |
| miRanComp | miRanComp comparison of mRNAs present with miRanda file... |
| miRanda | This is data is the results file from EBV miRanda... |
| miRandaIntersect | miRandaIntersect Looks for Intersection of Significant output... |
| mirandaIntersectInter | mirandaIntersectInter Looks for Intersection of Significant... |
| miRandaM | This is data is the results file from mouse miRanda... |
| miranda_sponge_predict | Transform miRanda data for relevant mRNA and miRNA to matrix... |
| miRNA | This is data is the miRNA expression file. This data set is... |
| miRNA0_2 | This is data is the miRNA0_2 FC for 0-2 time point. This data... |
| miRNA0_5 | This is data is the miRNA0_5 FC for 0-5 time point. This data... |
| miRNA2_5 | This is data is the miRNA2_5 FC for 2-5 time point. This data... |
| miRNA_fc | This is data is the combined miRNA FC for all time points.... |
| miRNA_fc2 | This data is the miRNA fold change data set for difference or... |
| mirRnaDensityCor | mirRnaDensityCor for miRTarRNASeq miRNA and mRNA correlation... |
| mirRnaDensityInter | mirRnaDensityInter for mirTarRnaSeq miRNA and mRNA... |
| mirRnaHeatmap | mirRnaHeatmap pheatmap for miRTarRNASeq miRNA and mRNA... |
| mirRnaHeatmapDiff | mirRnaHeatmapDiff heatmap for miRTarRNASeq miRNA and mRNA... |
| modelAIC | Obtain model AIC |
| modelCoefficients | Obtain coefficients |
| modelData | Obtain model input data |
| modelModelName | Obtain model name |
| modelModelPvalue | Obtain model p-value |
| modelsFilter | modelsFilter Filter a list of models based on logical... |
| modelTermPvalues | Obtain p-values for terms in model formula |
| mRNA | This is data is the mRNA expression file. This data set is... |
| mRNA0_2 | This is data is the mRNA0_2 FC for 0-2 time point. This data... |
| mRNA0_5 | This is data is the mRNA0_5 FC for 0-5 time point. This data... |
| mRNA2_5 | This is data is the mRNA2_5 FC for 2-5 time point. This data... |
| mRNA_fc | This is data is the combined mRNA FC for all time points.... |
| mRNA_fc2 | This data is the mRNA fold change data set for difference or... |
| one2manySponge | Sparse Partial Correlations On mRNA/miRNA Expression We make... |
| one2OneRnaMiRNA | one2OneRnaMiRNA correlation for miRNA and mRNA using... |
| outs | This is data is the output file resulted from time... |
| outs2 | This is data is the output file resulted from time... |
| plotFit | Plot model |
| plotResiduals | Plot residuals |
| plotTerms | plotTerms |
| results | This is data is the output file resulted from time point or... |
| runAllMirnaModels | runAllMirnaModels runModel for all miRNAs |
| runModel | Run a model of a specific kind |
| runModels | runModels runs miRNA mrna model model for various miRNA-mRNA... |
| sampCorRnaMirna | sampCorRnaMirna sampling for correlation for miRNA and mRNA |
| sig_corrs | This is data is the output file resulted from time point or... |
| sig_InterR | This is data is the output file resulted from time point or... |
| some_model | This is data is the results file from regression analysis and... |
| threshSig | threshSig Using shuffling threshold finds appropriate... |
| threshSigInter | threshSigInter Using shuffling threshold finds appropriate... |
| twoTimePoint | twoTimePoint miRNA and mRNA interrelation in two timepoints |
| twoTimePointSamp | twoTimePointSamp miRNA and mRNA interrelation in two... |
| tzTrans | tzTransTranspose and z-score transformation |
