Overview | Data setup | The fit_fn contract | Minimal example | Single-agent: apply_fit() | Writing to the Metrics assay | Idempotent merge | Coexisting fit sources | Reference Hill fit: fit_drug_response_metrics() | Numerical equivalence with fit_SE() | summary_fn: cell-level aggregation | Combination data: synergy scores | What fit_SE.combinations() does internally | Running all steps individually | Skipping a step | Two approaches for combination scoring in the new API | Approach 1: apply_combo_scores() — replicate fit_SE.combinations exactly | Approach 2: bliss_fit_fn / hss_fit_fn — simplified, no SA fits needed | Efficient multi-fit: apply_fits() | Shared pre-computation pattern | Chaining with pipe | Error handling | Time-course data: fit_SE.timecourse() | Inputs | Output structure | Custom fitting for time-course data | Key design notes | Provenance: how each fit was produced | Quick reference | Function signatures | fit_fn contract | summary_fn contract | Reference implementations | Single-agent fit functions (for apply_fit()) | Combination scoring | Composable step functions | Lower-level scoring functions (for apply_fit()) | SessionInfo

Introduction | Loading the gDR-generated MAE object | Converting the MAE object into a PharmacoSet object | TreatmentResponseExperiment Object | Row and Column Names | data.table Subsetting | assays | References

Overview | Loading a PharmacoSet (PSet) | Converting PharmacoSet to data.table for gDR pipeline | Subsetting to extract relevant information | Running drug response pipeline with data | SessionInfo

Introduction | R Packages | Data structures | Overview | Quick start | Aggregating raw data and metadata (1) | Transforming data into a SummarizedExperiment (2) | Averaging and fitting data (3) | runDrugResponseProcessingPipeline | Appendix | SessionInfo

What this vignette is | How an option reaches the browser | Loaders | Options every track accepts | Numeric tracks: bedGraph, wig, bigWig | Annotation tracks: bed, gff3 | Alignment tracks: bam, cram | Variant tracks: vcf | GWAS tracks | Splice junction tracks | Options on startup tracks | When an option seems to do nothing | Session Info

Overview | Introduction | Data model | Drug processing | Required columns | gDR pipeline | Use Cases | Data preprocessing | Running gDR pipeline | Data extraction | Custom fitting | apply_custom_fit() — generic interface | apply_fit_to_se() — single-agent convenience wrapper | Key features | Reference implementations | SessionInfo

Who this is for | Install | The three moving parts | A complete app | Loading a track from your own data | Loading tracks at startup | Drawing two tracks in one panel | Moving around, and knowing where you are | Inside a Shiny module | Stock genomes | Custom genomes | When something does not show up | Where to go next | Session Info

Overview | Content | Dose Response Plots | Single-agent Data | Combination Data | Metrics plot | Co-dilution Data | Quality Control | Merging of Manifest, Treatment and Raw data using gDRimport | Mapping Controls to Treated | Degree of Errors in Normalization Values | Averaged Values | Accuracy of Fitting Dose-response Curves | Quality Control - Fitting Precision | Correlation between PRISM and DepMap | Volcano plot | Scatter plot with correlation | Boxplots | SessionInfo

Overview | Use Cases | Synthetic data generation | Synthetic object of gDR data model | Annotation data | Other | SessionInfo

Introduction | Data Source & Citation | Data Overview | Data Dictionary | Models (Cell Line Metadata) | Somatic Mutations (Hotspot) | Somatic Mutations (Damaging) | CRISPR Gene Effect | Gene Expression | Copy Number Variation (CNV) | Important Limitations & Disclaimers | SessionInfo

General R code | General Shiny code | General package code | Git best practices | SessionInfo

Overview | Use Cases | Style guide | CI/CD | Package installation | SessionInfo

Overview | Use cases | Data manipulation | Data extraction | Managing gDR identifiers | Validating identifiers | Prettifying identifiers | Data validation | Prettifying | Colnames of data.table(s) | Assay names | SessionInfo

Introduction | General overview of the data model | Supported Experiments: | SummarizedExperiment objects: | MultiAssayExperiment object | SummarizedExperiment object | Assays | rowData | colData | metadata | Session info

Overview | Use Cases | Test Data | Load data | PRISM | Processing LEVEL5 PRISM Data | Processing LEVEL6 PRISM Data | Package installation | SessionInfo

Overview | Demostration: a local data.frame with 5 columns | Demonstration: a remote GWAS file with 34 columns | Session Info

Overview | Load the libraries we need | Display a list of the currently supported genomes | Display MYC | Create and display minimal 1-row data.frame centered below MYC on chr8 | Create and display a simulated quantitative (bedGraph) track | Zoom out by direct manipulation of the currently displayed region | Zoom out and by function calls | Session Info

Overview | Display a genomic region of interest in igvR | Query the AnnotationHub | Select Two Resources: boadPeaks and fc bigwig | broadPeaks: subset and display | bigWig: subset and display | Session Info

Overview | Display a genomic region of interest in igvR | Obtain the coordinates | Navigate the Table Browser | Examine the Data | Download the Data | Read the data into R | Create and Display a Quantitative Track | Session Info

Overview | Example | Code | Display | Session Info

Overview | Explicit loading of "custom" hg38 | Use the SARS-CoV-2 genome | Configure and run an nginx webserver, with CORS and Byte-Range support | CORS: cross-origin resource sharing | Byte-range support | A sample nginx configuration. | Run nginx out of a docker container. | Session Info

Overview | Demonstration | Display | Session Info

Overview | Load the libraries | Initialize igvR | Scenario 1: Loading a Remote CRAM File | Scenario 2: Visualizing Local CRAM Files | Step 1: Start a Local Web Server | Step 2: Load the Track using "localhost" | Session Info

Data Annotation Process for gDR Pipeline | Introduction | Annotation Files | Annotation File Locations | Annotation Requirements | Drug Annotation Requirements | Cell Line Annotation Requirements | Annotating SummarizedExperiment and MultiAssayExperiment Objects | Additional Information for Genentech/Roche Users | Conclusion | SessionInfo

Overview | Initialize igvR | Load alignments for the currently displayed genomic region | Display the alignment | Narrow Peaks from MACS | Motif Matching | Display the Matches | H3K4Me3 Histone Marks | Zoom in to one interesting, and possibly functional CTCF binding site

Introduction | Standard Message Format | The Simple BrowserViz ``Application''