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

## Documentation for package ‘BioTIP’ version 1.0.0

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

## Help Pages

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