# Calculate and Visualize Synergy Scores for Drug Combinations

## Documentation for package ‘synergyfinder’ version 3.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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