Package: BioTIP 1.26.0

Felix Yu

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

Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.

Authors:Zhezhen Wang, Andrew Goldstein, Yuxi Sun, Biniam Feleke, Qier An, Antonio Feliciano, Xinan Yang

BioTIP_1.26.0.tar.gz
BioTIP_1.26.0.zip(r-4.7)BioTIP_1.26.0.zip(r-4.6)BioTIP_1.26.0.zip(r-4.5)
BioTIP_1.26.0.tgz(r-4.6-any)BioTIP_1.26.0.tgz(r-4.5-any)
BioTIP_1.26.0.tar.gz(r-4.7-any)BioTIP_1.26.0.tar.gz(r-4.6-any)
BioTIP_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BioTIP/json (API)

# Install 'BioTIP' in R:

install.packages('BioTIP', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/xyang2uchicago/biotip/issues

Datasets:

cod - Cod dataset
gencode - A chr21 data from GENCODE GRCh37
GSE6136_cli - GSE6136 cli dataset
GSE6136_matrix - GSE6136 matrix dataset
ILEF - Chromosome ranges of chr21 dataset
intron - Coding transcriptome in chr21 dataset

On BioConductor:BioTIP-1.27.0(bioc 3.24)BioTIP-1.26.0(bioc 3.23)

sequencing rnaseq geneexpression transcription software

7.25 score 24 stars 37 scripts 436 downloads 25 exports 64 dependencies

Last updated from:9c5c23bc26 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	180
linux-devel-x86_64	WARNING	234
source / vignettes	OK	285
linux-release-x86_64	WARNING	292
macos-release-arm64	WARNING	111
macos-oldrel-arm64	WARNING	129
windows-devel	WARNING	157
windows-release	WARNING	160
windows-oldrel	WARNING	151
wasm-release	OK	148

Exports:avg.cor.shrink cor.shrink getBiotypes getCluster_methods getCTS getIc getIc.new getMaxMCImember getMaxStats getMCI getNetwork getNextMaxStats getReadthrough getTopMCI optimize.sd_selection plot_Ic_Simulation plot_MCI_Simulation plot_SS_Simulation plotBar_MCI plotIc plotMaxMCI sd_selection simulation_Ic simulation_Ic_sample simulationMCI

Dependencies:abind assorthead beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster cli cluster codetools cpp11 DelayedArray doParallel dqrng edgeR foreach formatR futile.logger futile.options generics GenomicRanges glue GPArotation igraph IRanges irlba iterators lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats metapod mnormt nlme pkgconfig psych Rcpp rlang rsvd S4Arrays S4Vectors ScaledMatrix scran scuttle Seqinfo SingleCellExperiment sitmo snow SparseArray statmod stringi stringr SummarizedExperiment vctrs XVector

BioTIP: an R-package for Characterization of Biological Tipping-Points

Zhezhen Wang, Andrew Goldstein, Yuxi Sun, Biniam Feleke, Qier An, Antonio Feliciano, Ieva Tolkaciovaite, and Xinan H Yang

Rendered fromBioTIP.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-05-16
Started: 2019-08-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Estimation of average values of correlation	avg.cor.shrink
cod dataset	cod
Estimation of correlation matrix	cor.shrink
A chr21 data from GENCODE GRCh37	gencode
Assigning Transcript Biotypes	getBiotypes
Clustering Network Nodes	getCluster_methods
Obtain the identified BioTiP and its length	getCTS
Get Index for Critical transition (Ic score)	getIc
Index of criticality Scoring System with estimated correlation, an updated Ic-score	getIc.new
Identifying the 'Biomodule'	getMaxMCImember
Get the cluster index and network nodes of biomodule	getMaxStats
Calculating MCI Scores	getMCI
Calculating MCI Score for randomly selected	getMCI_inner
Building Networks of Nodes	getNetwork
Overlapping Coding Regions	getReadthrough
GSE6136 cli dataset	GSE6136_cli
GSE6136 matrix dataset	GSE6136_matrix
Chromosome ranges of chr21 dataset	ILEF
Coding transcriptome in chr21 dataset	intron
Optimization of sd selection	optimize.sd_selection
Line or boxplot of an observed and its simulated scores	plot_Ic_Simulation
Plot observed and simulated MCI Scores	plot_MCI_Simulation
Density plot the leading two distance between any two states from random scores of all states in a system.	plot_SS_Simulation
plot MCI barplots	plotBar_MCI
plot a line plot of Ic scores for each state.	plotIc
Plot the Maximized MCI per State	plotMaxMCI
Selecting Highly Oscillating Transcripts	sd_selection
Calculating random Index of Critical transition (Ic scores) for randomly-selectd genes	simulation_Ic
Calculating (and plot) random Ic scores (Mojtahedi et al. 2016) based on shuffling sample labelling.	simulation_Ic_sample
Get MCI Scores for randomly selected genes	simulationMCI