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

Introduction | Creating a RadioSet | Basic Functionalities of RadioGx | Installing RadioGx | RadioSet | Accessing Data | Accessing metadata | Accessing molecular data | Accessing response data | Fitting Linear Quadratic (LQ) Models | Calculating Dose-Response Metrics | Dose-Response Curves | Summarizing Sensitivity | Summarizing Molecular Data | Molecular Signatures for Biomarker Discovery

CoreGx | Importing and Using CoreGx | The CoreSet Class | Extending the CoreSet Class | sessionInfo

Why Do We Need A New Class? | Design Philosophy | Anatomy of a TreatmentResponseExperiment | Class Diagram | Object Structure and Cardinality | Constructing a TreatmentResponseExperiment | The DataMapper Class | The TREDataMapper Class | metaConstruct Method | TreatmentResponseExperiment Object | Row and Column Names | data.frame Subsetting | Regex Queries | data.table Subsetting | Accessor Methods | rowData | colData | assays | assay | References | sessionInfo

Plotting gene expression changes from TG-GATEs dataset | Connectivity map analysis on TG-GATEs and human hepatocarcinoma signatures

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

Introduction | Loading Package for Case Studies | Load Datasets and Packages for Case Studies | Case Studies | Compare Molecular Subtype Classifications | Comparing Risk Prediction Models | References | Where genefu was used in subtyping | Where genefu was used in Comparing Subtyping Schemes | Where genefu was used to Compute Prognostic gene signature scores | As well as other publications | SessionInfo

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

Introduction | A use case: from expression data to survival analysis | Session Info | Functions within SurvComp