Calculate and Visualize Synergy Scores for Drug Combinations

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Documentation for package ‘synergyfinder’ version 3.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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