Package: BIGL 1.8.0

Maxim Nazarov

BIGL: Biochemically Intuitive Generalized Loewe Model

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.

Authors:Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas, Stijn Hawinkel, Javier Franco Pérez

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BIGL.pdf |BIGL.html✨
BIGL/json (API)
NEWS

# Install 'BIGL' in R:
install.packages('BIGL', repos = c('https://openanalytics.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/openanalytics/bigl/issues

Datasets:

On CRAN:

6.02 score 7 stars 37 scripts 641 downloads 2 mentions 16 exports 79 dependencies

Last updated 1 years agofrom:e6e06d9348. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winNOTENov 14 2024
R-4.5-linuxNOTENov 14 2024
R-4.4-winNOTENov 14 2024
R-4.4-macNOTENov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:constructFormulafitMarginalsfitSurfacegenerateDatagetTransformationsinitialMarginalisobologramoptim.boxcoxoutsidePointsplotConfIntplotMeanVarFitplotResponseSurfacepredictOffAxisrunBIGLsimulateNullsynergy_plot_bycomp

Dependencies:askpassbase64encbslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tableDEoptimRdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimeminpack.lmmunsellnleqslvnlmenumDerivopensslpillarpkgconfigplotlyprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbasesassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Methodology

Rendered frommethodology.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2020-12-16
Started: 2017-06-28

Synergy analysis

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-06-13
Started: 2017-06-28

Readme and manuals

Help Manual

Help pageTopics
Add residuals by adding to mean effectsaddResids
Backscale residualsbackscaleResids
Bliss Independence ModelBlissindependence
Obtain confidence intervals for the raw effect sizes on every off-axis point and overallbootConfInt
Apply two-parameter Box-Cox transformationboxcox.transformation
Coefficients from marginal model estimationcoef.MarginalFit
R color to RGB (red/green/blue) conversion.col2hex
Construct a model formula from parameter constraint matrixconstructFormula
Method for plotting of contours based on maxR statisticscontour.ResponseSurface
Residual degrees of freedom in marginal model estimationdf.residual.MarginalFit
Partial data with combination experiments of direct-acting antiviralsdirectAntivirals
Full data with combination experiments of direct-acting antiviralsdirectAntivirals_ALL
Fit two 4-parameter log-logistic functions for a synergy experimentfitMarginals
Fit response surface model and compute meanR and maxR statisticsfitSurface
Compute fitted values from monotherapy estimationfitted.MarginalFit
Predicted values of the response surface according to the given null modelfitted.ResponseSurface
Compute combined predicted response from drug doses according to standard or generalized Loewe model.generalizedLoewe
Generate data from parameters of marginal monotherapy modelgenerateData
Return absolute t-value, used in optimization call in 'optim.boxcox'get.abs_tval
Summarize data by factorget.summ.data
Estimate CP matrix from bootstrapsgetCP
A function to get the d1d2 identifiergetd1d2
Helper functions for the test statisticsgetR
Estimate initial values for dose-response curve fitGetStartGuess
Return a list with transformation functionsgetTransformations
Alternative Loewe generalizationharbronLoewe
Highest Single Agent modelhsa
Estimate initial values for fitting marginal dose-response curvesinitialMarginal
Isobologram of the response surface predicted by the null modelisobologram
4-parameter logistic dose-response functionL4
Fit two 4-parameter log-logistic functions with non-linear least squaresmarginalNLS
Fit two 4-parameter log-logistic functions with common baselinemarginalOptim
Compute maxR statistic for each off-axis dose combinationmaxR
Compute meanR statistic for the estimated modelmeanR
Calculate model variance, assuming variance increases linearly with meanmodelVar
Find optimal Box-Cox transformation parametersoptim.boxcox
List non-additive pointsoutsidePoints
Plot confidence intervals in a contour plotplot.BIGLconfInt
Plot of effect-size objectplot.effect-size
Plot monotherapy curve estimatesplot.MarginalFit
Plot of maxR objectplot.maxR
Plot bootstrapped cumulative distribution function of meanR null distributionplot.meanR
Method for plotting response surface objectsplot.ResponseSurface
Plot confidence intervals from BIGL object in a contour plotplotConfInt
Make a mean-variance plotplotMeanVarFit
Plot response surfaceplotResponseSurface
Predict values on the dose-response curvepredict.MarginalFit
Compute off-axis predictionspredictOffAxis
Predict the entire response surface, so including on-axis points, and return the result as a matrix. For plotting purposes.predictResponseSurface
Predict variancepredictVar
Print summary of BIGLconfInt objectprint.summary.BIGLconfInt
Print method for summary of 'MarginalFit' objectprint.summary.MarginalFit
Print summary of maxR objectprint.summary.maxR
Print summary of meanR objectprint.summary.meanR
Print method for the summary function of 'ResponseSurface' objectprint.summary.ResponseSurface
Residuals from marginal model estimationresiduals.MarginalFit
Run the BIGL application for demonstrating response surfacesrunBIGL
Sample residuals according to a new modelsampleResids
Functions for scaling, and rescaling residuals. May lead to unstable behaviour in practicescaleResids
Simulate data from a given null model and monotherapy coefficientssimulateNull
Summary of confidence intervals objectsummary.BIGLconfInt
Summary of 'MarginalFit' objectsummary.MarginalFit
Summary of maxR objectsummary.maxR
Summary of meanR objectsummary.meanR
Summary of 'ResponseSurface' objectsummary.ResponseSurface
Plot 2D cross section of response surfacesynergy_plot_bycomp
Estimate of coefficient variance-covariance matrixvcov.MarginalFit