GSE6136_cli             GSE6136 cli dataset
GSE6136_matrix          GSE6136 matrix dataset
ILEF                    Chromosome ranges of chr21 dataset
avg.cor.shrink          Estimation of average values of correlation
cod                     cod dataset
cor.shrink              Estimation of correlation matrix
gencode                 A chr21 data from GENCODE GRCh37
getBiotypes             Assigning Transcript Biotypes
getCTS                  Obtain the identified BioTiP and its length
getCluster_methods      Clustering Network Nodes
getIc                   Get Index for Critical transition (Ic score)
getIc.new               Index of criticality Scoring System with
                        estimated correlation, an updated Ic-score
getMCI                  Calculating MCI Scores
getMCI_inner            Calculating MCI Score for randomly selected
getMaxMCImember         Identifying the 'Biomodule'
getMaxStats             Get the cluster index and network nodes of
                        biomodule
getNetwork              Building Networks of Nodes
getReadthrough          Overlapping Coding Regions
intron                  Coding transcriptome in chr21 dataset
optimize.sd_selection   Optimization of sd selection
plotBar_MCI             plot MCI barplots
plotIc                  plot a line plot of Ic scores for each state.
plotMaxMCI              Plot the Maximized MCI per State
plot_Ic_Simulation      Line or boxplot of an observed and its
                        simulated scores
plot_MCI_Simulation     Plot observed and simulated MCI Scores
plot_SS_Simulation      Density plot the leading two distance between
                        any two states from random scores of all states
                        in a system.
sd_selection            Selecting Highly Oscillating Transcripts
simulationMCI           Get MCI Scores for randomly selected genes
simulation_Ic           Calculating random Index of Critical transition
                        (Ic scores) for randomly-selectd genes
simulation_Ic_sample    Calculating (and plot) random Ic scores
                        (Mojtahedi et al. 2016) based on shuffling
                        sample labelling.
