Man pages for xyang2uchicago/BioTIP
BioTIP: An R package for characterization of Biological Tipping-Point
| avg.cor.shrink | Estimation of average values of correlation |
| BioTIP-package | BioTIP: BioTIP: An R package for characterization of... |
| cod | cod dataset |
| cor.shrink | Estimation of correlation matrix |
| 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 Index for Critical transition (Ic score) |
| getIc.new | Index of criticality Scoring System with estimated... |
| getMaxMCImember | Identifying the 'Biomodule' |
| getMaxStats | Get the cluster index and network nodes of biomodule |
| getMCI | Calculating MCI Scores |
| getMCI_inner | Calculating MCI Score for randomly selected |
| 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. |
| plot_Ic_Simulation | Line or boxplot of an observed and its simulated scores |
| plotMaxMCI | Plot the Maximized MCI per State |
| plot_MCI_Simulation | Plot observed and simulated MCI Scores |
| plot_SS_Simulation | Density plot the leading two distance between any two states... |
| sd_selection | Selecting Highly Oscillating Transcripts |
| simulation_Ic | Calculating random Index of Critical transition (Ic scores)... |
| simulation_Ic_sample | Calculating (and plot) random Ic scores (Mojtahedi et al.... |
| simulationMCI | Get MCI Scores for randomly selected genes |
