Summary | 1 Installation | 2 Input data | 3 Reshaping and pre-processing | 4 Synergy and sensitivity analysis | 4.0 Baseline Correction | 4.1 Drug synergy scoring | 4.2 Sensitivity scoring | 5 Visualization | 5.1 Dose-response curve | 5.2 Two-drug combination visualization | 5.2.1 Heatmap | 5.2.2 2D contour plot | 5.2.3 3D surface plot | 5.3 Plotting wrapper for two-drug combination | 5.4 Synergy barometer | 5.5 Barplot | 5.6 SS plot | 6 Data with replicates | 6.1 Reshaping and pre-processing | 6.2 Drug synergy scoring | 6.3 Sensitivity scoring | 6.4 Visualization | 7 Higher-order drug combination screening | 7.1 Reshaping and pre-processing | 7.2 Drug synergy scoring | 7.3 Sensitivity scoring | 7.4 Visualization | Citation | For use of SynergyFinder R package or web application: | For use of ZIP synergy scoring: | For how to harmonize the different synergy scoring methods: | For general ideas of drug combination therapies: | For retrieving the most comprehensive drug combination data resources and their sensitivity and synergy results by SynergyFinder, please go to DrugComb : | For use of combination sensitivity score: | Reference
Package: synergyfinder 3.21.0
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:
synergyfinder_3.21.0.tar.gz
synergyfinder_3.21.0.zip(r-4.7)synergyfinder_3.21.0.zip(r-4.6)synergyfinder_3.21.0.zip(r-4.5)
synergyfinder_3.21.0.tgz(r-4.6-any)synergyfinder_3.21.0.tgz(r-4.5-any)
synergyfinder_3.21.0.tar.gz(r-4.7-any)synergyfinder_3.21.0.tar.gz(r-4.6-any)
synergyfinder_3.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
synergyfinder/json (API)
| # Install 'synergyfinder' in R: |
| install.packages('synergyfinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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
On BioConductor:synergyfinder-3.21.0(bioc 3.24)synergyfinder-3.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ebf173dc52. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 199 | ||
| linux-devel-x86_64 | WARNING | 299 | ||
| source / vignettes | OK | 363 | ||
| linux-release-x86_64 | WARNING | 257 | ||
| macos-release-arm64 | WARNING | 140 | ||
| macos-oldrel-arm64 | WARNING | 154 | ||
| windows-devel | WARNING | 161 | ||
| windows-release | WARNING | 172 | ||
| windows-oldrel | WARNING | 184 | ||
| wasm-release | OK | 217 |
Exports:.AdjustColumnName.ExtractMultiDrugPlotDataBlissCalculateCSSCalculateIC50CalculateRICalculateSensitivityCalculateSynergyCorrectBaseLineDimensionReductionExtractSingleDrugFindModelParFindModelTypeFitDoseResponseGenerateSurfaceHighlightBarPlotHSAImputeIC50LoewePlot2DrugContourPlot2DrugHeatmapPlot2DrugSurfacePlotBarometerPlotDoseResponsePlotDoseResponseCurvePlotMultiDrugBarPlotMultiDrugSurfacePlotSensitivitySynergyPlotSynergyPredictResponseReshapeDataZIP
Dependencies:abindaskpassbackportsbase64encbitbit64blobbootbroombslibcachemcallrcarcarDatacellrangercheckmateclassclassIntclicliprclustercodetoolscolorspaceconflictedcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDerivdigestdoBydotCall64dplyrdrcdtplyre1071evaluatefarverfastmapfieldsFNNfontawesomeforcatsforeachforecastFormulaformula.toolsfracdifffsfurrrfuturegarglegenericsggforceggplot2ggrepelglmnetglobalsgluegoogledrivegooglesheets4gstatgtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttridsintervalsisobanditeratorsjomojquerylibjsonliteKernSmoothknitrkriginglabelinglaterlatticelazyevallifecyclelistenvlme4lmtestlubridatemagrittrmapsMASSMatrixMatrixModelsmemoisemetRmgcvmicemimeminqamitmlmodelrmultcompmvtnormnleqslvnlmenloptrnnetnumDerivopenssloperator.toolsordinalotelpanparallellypbapplypbkrtestpermutepillarpkgconfigplotlyplotrixplyrpolyclipprettyunitsprocessxprogresspromisesproxypspurrrquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchrematch2reprexreshape2rlangrmarkdownrpartrstudioapirvests2S7sandwichsassscalesselectrsfsftimeshapespspacetimespamSparseMSpatialExtremesstarsstringistringrsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttidyversetimechangetimeDatetinytextweenrtzdbucminfunitsurcautf8uuidvctrsveganviridisLitevroomwithrwkxfunxml2xtsyamlzoo
