Introduction | PharmacoSet Structure | sample | treatment | curation: | molecularProfiles: | datasetType | treatmentResponse: | New in PharmacoGx 2.0 | Old in PharmacoGx 1.0 | perturbation: | annotation | Creating the PharmacoSet | PharmacoGx 2.0 | PharmacoGx 1.0

Introduction | Load Data | Subtyping | Subtype Scores

Synergy/Antagonism Biomarker Discovery | Mathews Griner | Reading in Raw Data | Experimental Design Hypothesis | Handling Undocumented Replicates | Using the TREDataMapper | Creating a TreatmentResponseExperiment | Normalizing Treatment Response | Fitting Monotherapy Curves | Joining Monotherapy Curve Fits to Combinations | Compute Synergy Scores | Visualizing Drug Synergy | Session Info | References

Introduction | Installation and Settings | Requirements | Downloading PharmacoSet Objects | Downlading Drug Signatures | Case Study | (In)Consistency across large pharmacogenomic studies | Query the Connectivity Map | Estimating Drug Sensitivity Measures | Curve Fitting | Plotting Drug-Dose Response Data | Gene-Drug Association Modelling | Sensitivity Modelling | Perturbation Modelling | Connectivity Scoring | GSEA | GWC | Acknowledgements | Session Info | References

1 Introduction | 2 Installation and Settings | 3 Definitions | 4 Data Access | 5 Visualizing PDX Growth Curve | 6 Replicate-based PDX experiments | 7 PDX Model Drug Response | 8 Gene-drug association | 9 Creating new Xeva object | 10 SessionInfo

Pancreatic Cancer Overall Survival Predictor | Split Training and Validation Data | Setup A PCOSP Model Object | Training a PCOSP Model | Risk Prediction with a PCOSP Model | Validating A PCOSP Model | Plotting Model Performance | Permutations Testing for a PCOSP Model | Random Label Shuffling Model | Construct the Model Object | Train the Model | Predict the Classes | Validate Model Performance | Compare with a PCOSP Model | Random Gene Assignment Model | Compare RGAModel to PCOSP | Pathway Analysis of a PCOSP Model | Get the Top Predictive Features | Querying Genesets for Enriched Pathways | Clinical Model Comparison | Build the Model | Validate the Model | Visualize Comparison with PCOSP Model | Comparing PCOSP Models to Existing Published Classifiers | Make the Models | Validate the Models | Model Performance Meta-Analysis | Comparing PCOSP Models By Patient Subtype | References

Overview | Installation | Classes | SurvivalExperiment | Constructor | Accessors | CohortList | SurivivalModel | Sub-Classes | References