Package: BIGL 1.9.2

Kathy Mutambanengwe

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, Kathy Mutambanengwe

BIGL_1.9.2.tar.gz
BIGL_1.9.2.tar.gz(r-4.5-noble)BIGL_1.9.2.tar.gz(r-4.4-noble)
BIGL_1.9.2.tgz(r-4.4-emscripten)BIGL_1.9.2.tgz(r-4.3-emscripten)
BIGL.pdf |BIGL.html✨
BIGL/json (API)
NEWS

# InstallBIGL in R:

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

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

Datasets:

directAntivirals - Partial data with combination experiments of direct-acting antivirals
directAntivirals_ALL - Full data with combination experiments of direct-acting antivirals

16 exports 0.36 score 79 dependencies 663 downloads

Last updated 9 days agofrom:2905641edf

Exports:constructFormula fitMarginals fitSurface generateData getTransformations initialMarginal isobologram optim.boxcox outsidePoints plotConfInt plotMeanVarFit plotResponseSurface predictOffAxis runBIGL simulateNull synergy_plot_bycomp

Dependencies:askpass base64enc bslib cachem cli colorspace cpp11 crayon crosstalk curl data.table DEoptimR digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime minpack.lm munsell nleqslv nlme numDeriv openssl pillar pkgconfig plotly prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown robustbase sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Methodology

Rendered frommethodology.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2023-12-21
Started: 2017-06-30

Synergy analysis

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-06-27
Started: 2017-06-30

Help page	Topics
Add residuals by adding to mean effects	addResids
Backscale residuals	backscaleResids
Bliss Independence Model	Blissindependence
Obtain confidence intervals for the raw effect sizes on every off-axis point and overall	bootConfInt
Apply two-parameter Box-Cox transformation	boxcox.transformation
Coefficients from marginal model estimation	coef.MarginalFit
R color to RGB (red/green/blue) conversion.	col2hex
Construct a model formula from parameter constraint matrix	constructFormula
Method for plotting of contours based on maxR statistics	contour.ResponseSurface
Residual degrees of freedom in marginal model estimation	df.residual.MarginalFit
Partial data with combination experiments of direct-acting antivirals	directAntivirals
Full data with combination experiments of direct-acting antivirals	directAntivirals_ALL
Fit two 4-parameter log-logistic functions for a synergy experiment	fitMarginals
Fit response surface model and compute meanR and maxR statistics	fitSurface
Compute fitted values from monotherapy estimation	fitted.MarginalFit
Predicted values of the response surface according to the given null model	fitted.ResponseSurface
Compute combined predicted response from drug doses according to standard or generalized Loewe model.	generalizedLoewe
Generate data from parameters of marginal monotherapy model	generateData
Return absolute t-value, used in optimization call in 'optim.boxcox'	get.abs_tval
Summarize data by factor	get.summ.data
Estimate CP matrix from bootstraps	getCP
A function to get the d1d2 identifier	getd1d2
Helper functions for the test statistics	getR
Estimate initial values for dose-response curve fit	GetStartGuess
Return a list with transformation functions	getTransformations
Alternative Loewe generalization	harbronLoewe
Highest Single Agent model	hsa
Estimate initial values for fitting marginal dose-response curves	initialMarginal
Isobologram of the response surface predicted by the null model	isobologram
4-parameter logistic dose-response function	L4
Fit two 4-parameter log-logistic functions with non-linear least squares	marginalNLS
Fit two 4-parameter log-logistic functions with common baseline	marginalOptim
Compute maxR statistic for each off-axis dose combination	maxR
Compute meanR statistic for the estimated model	meanR
Calculate model variance, assuming variance increases linearly with mean	modelVar
Find optimal Box-Cox transformation parameters	optim.boxcox
List non-additive points	outsidePoints
Plot confidence intervals in a contour plot	plot.BIGLconfInt
Plot of effect-size object	plot.effect-size
Plot monotherapy curve estimates	plot.MarginalFit
Plot of maxR object	plot.maxR
Plot bootstrapped cumulative distribution function of meanR null distribution	plot.meanR
Method for plotting response surface objects	plot.ResponseSurface
Plot confidence intervals from BIGL object in a contour plot	plotConfInt
Make a mean-variance plot	plotMeanVarFit
Plot response surface	plotResponseSurface
Predict values on the dose-response curve	predict.MarginalFit
Compute off-axis predictions	predictOffAxis
Predict the entire response surface, so including on-axis points, and return the result as a matrix. For plotting purposes.	predictResponseSurface
Predict variance	predictVar
Print summary of BIGLconfInt object	print.summary.BIGLconfInt
Print method for summary of 'MarginalFit' object	print.summary.MarginalFit
Print summary of maxR object	print.summary.maxR
Print summary of meanR object	print.summary.meanR
Print method for the summary function of 'ResponseSurface' object	print.summary.ResponseSurface
Residuals from marginal model estimation	residuals.MarginalFit
Run the BIGL application for demonstrating response surfaces	runBIGL
Sample residuals according to a new model	sampleResids
Functions for scaling, and rescaling residuals. May lead to unstable behaviour in practice	scaleResids
Simulate data from a given null model and monotherapy coefficients	simulateNull
Summary of confidence intervals object	summary.BIGLconfInt
Summary of 'MarginalFit' object	summary.MarginalFit
Summary of maxR object	summary.maxR
Summary of meanR object	summary.meanR
Summary of 'ResponseSurface' object	summary.ResponseSurface
Plot 2D cross section of response surface	synergy_plot_bycomp
Estimate of coefficient variance-covariance matrix	vcov.MarginalFit
Sample residuals according to a new model	wildbootAddResids

Package: BIGL 1.9.2

BIGL:Biochemically Intuitive Generalized Loewe Model

Methodology

Synergy analysis

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)