├── .github ├── .gitignore └── workflows │ ├── build-vignettes.yml │ ├── check-bioc.yml │ └── check-bioc.yml.old ├── .gitignore ├── DESCRIPTION ├── Meta └── vignette.rds ├── NAMESPACE ├── NEWS ├── R ├── XevaSet_Class.R ├── access_expressionData_Functions.R ├── access_slot_drug.R ├── access_slot_expDesign.R ├── access_slot_experiment.R ├── access_slot_modToBiobase.R ├── access_slot_model.R ├── access_slot_sensitivity.R ├── auc.R ├── create_Experiment_slot.R ├── create_expDesign_slot.R ├── data.R ├── downloadXevaSet.R ├── drug_Sensitivity_Signature.R ├── expDesign_manuplation.R ├── geneDrug_association.R ├── get_model_batch_data.R ├── important_functions.R ├── lmm.R ├── mRECIST.R ├── pdx_model_class.R ├── plot_functions.R ├── plot_mRECIST.R ├── response_matrices.R ├── slope_and_angle.R ├── subset_Xeva.R ├── summ_response_Function.R ├── tgi.R └── waterfall_plot.R ├── README.md ├── Rplots.pdf ├── data ├── PDXMI.rda ├── brca.rda └── repdx.rda ├── doc ├── Xeva.R ├── Xeva.Rnw └── Xeva.pdf ├── inst └── extdata │ ├── batch_list.rds │ ├── drug.csv │ ├── experiments.csv │ ├── model.csv │ ├── modelToExpressionMap.csv │ └── rnaseq.rds ├── man ├── ABC.Rd ├── AUC.Rd ├── PDXMI.Rd ├── TGI.Rd ├── addExperimentalDesign.Rd ├── angle.Rd ├── batchInfo.Rd ├── brca.Rd ├── createXevaSet.Rd ├── dosePlot.Rd ├── downloadXevaSet.Rd ├── drugInform.Rd ├── drugSensitivitySig.Rd ├── getExperiment.Rd ├── getMolecularProfileAssay.Rd ├── getMolecularProfiles.Rd ├── lmm.Rd ├── mRECIST.Rd ├── modelInfo.Rd ├── plotPDX.Rd ├── plotmRECIST.Rd ├── print.batchResponse.Rd ├── print.modelResponse.Rd ├── print.pdxBatch.Rd ├── repdx.Rd ├── response.Rd ├── selectModelIds.Rd ├── sensitivity.Rd ├── setResponse.Rd ├── slope.Rd ├── subsetXeva.Rd ├── summarizeMolecularProfiles.Rd ├── summarizeResponse.Rd └── waterfall.Rd └── vignettes ├── Xeva.Rnw ├── XevaBiblio.bib └── images └── Xeva_batch_2.pdf /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | 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