Package: BioTIP 1.19.0

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

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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'))

Peer review:

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

Datasets:

On BioConductor:BioTIP-1.19.0(bioc 3.20)BioTIP-1.18.0(bioc 3.19)

bioconductor-package

25 exports 1.16 score 73 dependencies

Last updated 22 days agofrom:04dae3a4ee

Exports:avg.cor.shrinkcor.shrinkgetBiotypesgetCluster_methodsgetCTSgetIcgetIc.newgetMaxMCImembergetMaxStatsgetMCIgetNetworkgetNextMaxStatsgetReadthroughgetTopMCIoptimize.sd_selectionplot_Ic_Simulationplot_MCI_Simulationplot_SS_SimulationplotBar_MCIplotIcplotMaxMCIsd_selectionsimulation_Icsimulation_Ic_samplesimulationMCI

Dependencies:abindaskpassbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblustercliclustercodetoolscpp11crayoncurlDelayedArrayDelayedMatrixStatsdqrngedgeRformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesirlbajsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmimemnormtnlmeopensslpkgconfigpsychR6RcppRcppHNSWrlangrsvdS4ArraysS4VectorsScaledMatrixscranscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

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 Jun 20 2024.

Last update: 2024-06-19
Started: 2019-08-19

Readme and manuals

Help Manual

Help pageTopics
Estimation of average values of correlationavg.cor.shrink
cod datasetcod
Estimation of correlation matrixcor.shrink
A chr21 data from GENCODE GRCh37gencode
Assigning Transcript BiotypesgetBiotypes
Clustering Network NodesgetCluster_methods
Obtain the identified BioTiP and its lengthgetCTS
Get Index for Critical transition (Ic score)getIc
Index of criticality Scoring System with estimated correlation, an updated Ic-scoregetIc.new
Identifying the 'Biomodule'getMaxMCImember
Get the cluster index and network nodes of biomodulegetMaxStats
Calculating MCI ScoresgetMCI
Calculating MCI Score for randomly selectedgetMCI_inner
Building Networks of NodesgetNetwork
Overlapping Coding RegionsgetReadthrough
GSE6136 cli datasetGSE6136_cli
GSE6136 matrix datasetGSE6136_matrix
Chromosome ranges of chr21 datasetILEF
Coding transcriptome in chr21 datasetintron
Optimization of sd selectionoptimize.sd_selection
Line or boxplot of an observed and its simulated scoresplot_Ic_Simulation
Plot observed and simulated MCI Scoresplot_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 barplotsplotBar_MCI
plot a line plot of Ic scores for each state.plotIc
Plot the Maximized MCI per StateplotMaxMCI
Selecting Highly Oscillating Transcriptssd_selection
Calculating random Index of Critical transition (Ic scores) for randomly-selectd genessimulation_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 genessimulationMCI