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

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Documentation for package ‘BioTIP’ version 1.16.0

• 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.