Calculate and Visualize Synergy Scores for Drug Combinations


[Up] [Top]

Documentation for package ‘synergyfinder’ version 3.12.0

Help Pages

.AdjustColumnName Adjust Column Names of Input Data Table
.Bootstrapping Bootstraping Sample from Replicates in Response Data
.Distance Calculate Distance from a Point to a Plane
.ExtendedScores Make a Smooth Surface for Scores
.Extract2DrugPlotData Extract Data for 2 Drug Combination Plots
.ExtractMultiDrugPlotData Extract Data Table and Annotation Information for Multi-drug Plotting
.Own_log CSS Facilitate Function - Log Calculation (nature based) LL.4 Model
.Own_log2 CSS Facilitate Function - Log (nature based) Calculation L.4 Model
.PredictResponseFromModel Predict Response Value at Certain Drug Dose
.Pt2mm Convert Font Size from pt to mm
.RoundValues Round the Numbers for Plotting
.ScoreCurve CSS Facilitate Function - .ScoreCurve for Curves Fitted by LL.4 Model
.ScoreCurve_L4 CSS Facilitate Function - .ScoreCurve for Curves Fitted by L.4 Model
.SolveExpDoesL4 Solve the Expected Dose of Drug to Achieve Given Effect from L.4 Model
.SolveExpDoesLL4 Solve the Expected Dose of Drug to Achieve Given Effect from LL.4 Model
.SolveExpDose Solve the Expected Dose of Drug to Achieve Given Effect (% inhibition)
.SolveLoewe Solve the Loewe Additive Effect for Concentration Combinations Isobologram
Bliss Calculate Bliss Synergy Score
CalculateCSS Calculate Combination Sensitivity Score
CalculateIC50 Calculate Relative IC50 from Fitted Model
CalculateRI Calculate Relative Inhibition (RI) for Dose-Response Curve
CalculateSensitivity Calculate the Sensitivity Scores for Drug Combinations
CalculateSynergy Calculate the Synergy Scores for Drug Combinations
CorrectBaseLine Base Line Correction for Drug Combination Matrix
DimensionReduction Dimension Reduction for Multi-drug Combination Visualization
ExtractSingleDrug Extract Single Drug Dose Response
FindModelPar Find the Fitted Parameters from 4-Parameter Log-Logistic Model
FindModelType Find the Type of Model Used for Fitting Dose Response Data
FitDoseResponse Fitting Single Drug Dose-Response Model
GenerateSurface 3D Surface Plot for Nulti-drug Combination Dose-Response/Synergy Scores
HighlightBarPlot Highlight Bars
HSA Calculate HSA Synergy Score
ImputeIC50 Impute Missing Value at IC50 Concentration of Drug
Loewe Calculate Loewe Synergy Score
mathews_screening_data A high-throughput drug combination screening data
NCATS_screening_data A high-throughput 3 drug combination screening data
ONEIL_screening_data A high-throughput 2 drugs combination screening data with replication
Plot2DrugContour 2D Contour Plot for 2-drug Combination Dose-Response/Synergy Scores
Plot2DrugHeatmap Heatmap Plot for 2-drug Combination Dose-Response/Synergy Scores
Plot2DrugSurface 3D Surface Plot for 2-drug Combination Dose-Response/Synergy Scores
PlotBarometer Plot Barometer for Responses at One Data Point
PlotDoseResponse Visualize the Drug Combination Dose-response Data
PlotDoseResponseCurve Plot Dose Response Curve for Single Drug
PlotMultiDrugBar Bar Plot for Multi-drug Combination Dose-Response/Synergy Scores
PlotMultiDrugSurface 3D Plot for Multi-drug Combination Dose-Response/Synergy Scores
PlotSensitivitySynergy Plot Sensitive-Synergy Plot for All the Combinations in the Input Data
PlotSynergy Plot Interaction Landscape for Synergy Scores
PredictResponse Predict Response Value at Certain Drug Dose
ReshapeData Pre-process the Response Data for Further Calculation and Plot
ZIP Calculate Delta Synergy Score Based on ZIP Model