# BioTIP: An R package for characterization of Biological Tipping-Point

## Documentation for package ‘BioTIP’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
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 correlation, an updated Ic-score
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.
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.