Package: BioTIP 1.21.0

Yuxi (Jennifer) Sun

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_1.21.0.tar.gz
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BioTIP.pdf |BioTIP.html✨
BioTIP/json (API)

# Install 'BioTIP' in R:

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

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

Datasets:

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

On BioConductor:BioTIP-1.21.0(bioc 3.21)BioTIP-1.20.0(bioc 3.20)

sequencing rnaseq geneexpression transcription software

6.84 score 18 stars 37 scripts 204 downloads 25 exports 73 dependencies

Last updated 2 months agofrom:3d67b56175. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	WARNING	Dec 19 2024
R-4.5-linux	WARNING	Dec 19 2024
R-4.4-win	WARNING	Dec 19 2024
R-4.4-mac	WARNING	Dec 19 2024
R-4.3-win	WARNING	Dec 19 2024
R-4.3-mac	WARNING	Dec 19 2024

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 askpass assorthead beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster cli cluster codetools cpp11 crayon curl DelayedArray dqrng edgeR formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue GPArotation httr igraph IRanges irlba jsonlite lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats metapod mime mnormt nlme openssl pkgconfig psych R6 Rcpp rlang rsvd S4Arrays S4Vectors ScaledMatrix scran scuttle SingleCellExperiment sitmo snow SparseArray statmod stringi stringr SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

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 Dec 19 2024.

Last update: 2024-06-19
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