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| cod | cod dataset |
| gencode | A chr21 data from GENCODE GRCh37 |
| getBiotypes | Assigning Transcript Biotypes |
| getCluster_methods | Clustering Network Nodes |
| getCTS | Obtain the identified BioTiP and its length |
| getIc | get Ic score |
| getMaxMCImember | Identifying the 'Biomodule' |
| getMaxStats | Get the cluster index and network nodes of biomodule |
| getMCI | Calculating MCI Scores |
| getNetwork | Building Networks of Nodes |
| getReadthrough | Overlapping Coding Regions |
| GSE6136_cli | GSE6136 cli dataset |
| GSE6136_matrix | GSE6136 matrix dataset |
| ILEF | Chromosome ranges of chr21 dataset |
| 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 plot of Ic score and simulated Ic scores |
| plot_MCI_Simulation | Simulation of Loci to Calculate the CI Score |
| plot_simulation_sample | calculating Ic scores based on simulated samples |
| sd_selection | Selecting Highly Oscillating Transcripts |
| simulationMCI | Get MCI Scores for Feature Permutation |
| simulation_Ic | calculating Ic scores based on simulated loci |