Package: synergyfinder 3.15.0

Shuyu Zheng

synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

Authors:Shuyu Zheng [aut, cre], Jing Tang [aut]

synergyfinder_3.15.0.tar.gz
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synergyfinder.pdf |synergyfinder.html✨
synergyfinder/json (API)
NEWS

# Install 'synergyfinder' in R:
install.packages('synergyfinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:synergyfinder-3.15.0(bioc 3.21)synergyfinder-3.14.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarestatisticalmethod

5.58 score 42 scripts 446 downloads 6 mentions 32 exports 196 dependencies

Last updated 2 months agofrom:b44cfae7f8. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winWARNINGNov 30 2024
R-4.5-linuxWARNINGNov 30 2024
R-4.4-winWARNINGNov 30 2024
R-4.4-macWARNINGNov 30 2024
R-4.3-winWARNINGNov 30 2024
R-4.3-macWARNINGNov 30 2024

Exports:.AdjustColumnName.ExtractMultiDrugPlotDataBlissCalculateCSSCalculateIC50CalculateRICalculateSensitivityCalculateSynergyCorrectBaseLineDimensionReductionExtractSingleDrugFindModelParFindModelTypeFitDoseResponseGenerateSurfaceHighlightBarPlotHSAImputeIC50LoewePlot2DrugContourPlot2DrugHeatmapPlot2DrugSurfacePlotBarometerPlotDoseResponsePlotDoseResponseCurvePlotMultiDrugBarPlotMultiDrugSurfacePlotSensitivitySynergyPlotSynergyPredictResponseReshapeDataZIP

Dependencies:abindaskpassbackportsbase64encbitbit64blobbootbroombslibcachemcallrcarcarDatacellrangercheckmateclassclassIntclicliprclustercodetoolscolorspaceconflictedcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDerivdigestdoBydotCall64dplyrdrcdtplyre1071evaluatefansifarverfastmapfieldsFNNfontawesomeforcatsforeachFormulaformula.toolsfsfurrrfuturegarglegenericsggforceggplot2ggrepelglmnetglobalsgluegoogledrivegooglesheets4gstatgtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttridsintervalsisobanditeratorsjomojquerylibjsonliteKernSmoothknitrkriginglabelinglaterlatticelazyevallifecyclelistenvlme4lubridatemagrittrmapsMASSMatrixMatrixModelsmemoisemetRmgcvmicemicrobenchmarkmimeminqamitmlmodelrmultcompmunsellmvtnormnleqslvnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanparallellypbapplypbkrtestpermutepillarpkgconfigplotlyplotrixplyrpolyclipprettyunitsprocessxprogresspromisesproxypspurrrquantregR6raggrappdirsRColorBrewerRcppRcppEigenreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrpartrstudioapirvests2sandwichsassscalesselectrsfsftimeshapespspacetimespamSparseMSpatialExtremesstarsstringistringrsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttidyversetimechangetinytextweenrtzdbucminfunitsutf8uuidvctrsveganviridisLitevroomwithrwkxfunxml2xtsyamlzoo

User tutorial of the SynergyFinder Plus

Shuyu Zheng, Wenyu Wang, and Jing Tang Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki

Rendered fromUser_tutorual_of_the_SynergyFinder_plus.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2022-11-01
Started: 2021-05-23

Readme and manuals

Help Manual

Help pageTopics
Adjust Column Names of Input Data Table.AdjustColumnName
Bootstraping Sample from Replicates in Response Data.Bootstrapping
Calculate Distance from a Point to a Plane.Distance
Make a Smooth Surface for Scores.ExtendedScores
Extract Data for 2 Drug Combination Plots.Extract2DrugPlotData
Extract Data Table and Annotation Information for Multi-drug Plotting.ExtractMultiDrugPlotData
CSS Facilitate Function - Log Calculation (nature based) LL.4 Model.Own_log
CSS Facilitate Function - Log (nature based) Calculation L.4 Model.Own_log2
Predict Response Value at Certain Drug Dose.PredictResponseFromModel
Convert Font Size from pt to mm.Pt2mm
Round the Numbers for Plotting.RoundValues
CSS Facilitate Function - .ScoreCurve for Curves Fitted by LL.4 Model.ScoreCurve
CSS Facilitate Function - .ScoreCurve for Curves Fitted by L.4 Model.ScoreCurve_L4
Solve the Expected Dose of Drug to Achieve Given Effect from L.4 Model.SolveExpDoesL4
Solve the Expected Dose of Drug to Achieve Given Effect from LL.4 Model.SolveExpDoesLL4
Solve the Expected Dose of Drug to Achieve Given Effect (% inhibition).SolveExpDose
Solve the Loewe Additive Effect for Concentration Combinations Isobologram.SolveLoewe
Calculate Bliss Synergy ScoreBliss
Calculate Combination Sensitivity ScoreCalculateCSS
Calculate Relative IC50 from Fitted ModelCalculateIC50
Calculate Relative Inhibition (RI) for Dose-Response CurveCalculateRI
Calculate the Sensitivity Scores for Drug CombinationsCalculateSensitivity
Calculate the Synergy Scores for Drug CombinationsCalculateSynergy
Base Line Correction for Drug Combination MatrixCorrectBaseLine
Dimension Reduction for Multi-drug Combination VisualizationDimensionReduction
Extract Single Drug Dose ResponseExtractSingleDrug
Find the Fitted Parameters from 4-Parameter Log-Logistic ModelFindModelPar
Find the Type of Model Used for Fitting Dose Response DataFindModelType
Fitting Single Drug Dose-Response ModelFitDoseResponse
3D Surface Plot for Nulti-drug Combination Dose-Response/Synergy ScoresGenerateSurface
Highlight BarsHighlightBarPlot
Calculate HSA Synergy ScoreHSA
Impute Missing Value at IC50 Concentration of DrugImputeIC50
Calculate Loewe Synergy ScoreLoewe
A high-throughput drug combination screening datamathews_screening_data
A high-throughput 3 drug combination screening dataNCATS_screening_data
A high-throughput 2 drugs combination screening data with replicationONEIL_screening_data
2D Contour Plot for 2-drug Combination Dose-Response/Synergy ScoresPlot2DrugContour
Heatmap Plot for 2-drug Combination Dose-Response/Synergy ScoresPlot2DrugHeatmap
3D Surface Plot for 2-drug Combination Dose-Response/Synergy ScoresPlot2DrugSurface
Plot Barometer for Responses at One Data PointPlotBarometer
Visualize the Drug Combination Dose-response DataPlotDoseResponse
Plot Dose Response Curve for Single DrugPlotDoseResponseCurve
Bar Plot for Multi-drug Combination Dose-Response/Synergy ScoresPlotMultiDrugBar
3D Plot for Multi-drug Combination Dose-Response/Synergy ScoresPlotMultiDrugSurface
Plot Sensitive-Synergy Plot for All the Combinations in the Input DataPlotSensitivitySynergy
Plot Interaction Landscape for Synergy ScoresPlotSynergy
Predict Response Value at Certain Drug DosePredictResponse
Pre-process the Response Data for Further Calculation and PlotReshapeData
Calculate Delta Synergy Score Based on ZIP ModelZIP