Man pages for shuyuzheng/synergyfinder
Calculate and Visualize Synergy Scores for Drug Combinations
| 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 |
| dot-AdjustColumnName | Adjust Column Names of Input Data Table |
| dot-Bootstrapping | Bootstraping Sample from Replicates in Response Data |
| dot-Distance | Calculate Distance from a Point to a Plane |
| dot-ExtendedScores | Make a Smooth Surface for Scores |
| dot-Extract2DrugPlotData | Extract Data for 2 Drug Combination Plots |
| dot-ExtractMultiDrugPlotData | Extract Data Table and Annotation Information for Multi-drug... |
| dot-Own_log | CSS Facilitate Function - Log Calculation (nature based) LL.4... |
| dot-Own_log2 | CSS Facilitate Function - Log (nature based) Calculation L.4... |
| dot-PredictResponseFromModel | Predict Response Value at Certain Drug Dose |
| dot-Pt2mm | Convert Font Size from pt to mm |
| dot-RoundValues | Round the Numbers for Plotting |
| dot-ScoreCurve | CSS Facilitate Function - .ScoreCurve for Curves Fitted by... |
| dot-ScoreCurve_L4 | CSS Facilitate Function - .ScoreCurve for Curves Fitted by... |
| dot-SolveExpDoesL4 | Solve the Expected Dose of Drug to Achieve Given Effect from... |
| dot-SolveExpDoesLL4 | Solve the Expected Dose of Drug to Achieve Given Effect from... |
| dot-SolveExpDose | Solve the Expected Dose of Drug to Achieve Given Effect (%... |
| dot-SolveLoewe | Solve the Loewe Additive Effect for Concentration... |
| ExtractSingleDrug | Extract Single Drug Dose Response |
| FindModelPar | Find the Fitted Parameters from 4-Parameter Log-Logistic... |
| 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... |
| 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... |
| Plot2DrugContour | 2D Contour Plot for 2-drug Combination Dose-Response/Synergy... |
| Plot2DrugHeatmap | Heatmap Plot for 2-drug Combination Dose-Response/Synergy... |
| Plot2DrugSurface | 3D Surface Plot for 2-drug Combination Dose-Response/Synergy... |
| 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... |
| PlotMultiDrugSurface | 3D Plot for Multi-drug Combination Dose-Response/Synergy... |
| PlotSensitivitySynergy | Plot Sensitive-Synergy Plot for All the Combinations in the... |
| 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... |
| ZIP | Calculate Delta Synergy Score Based on ZIP Model |
