Introduction | Installation | Reading profiles | Alleles are stored pre-split | Marker names | Metadata | Scoring | Comparing end to end | Mixing | Writing results | Querying Cellosaurus | The command line application | The Shiny application | STRprofilerR in a larger workflow | Bioconductor data structures | The bundled PDX database | Generating profiles from raw data | Carrying authentication info with an experiment | Maintaining a reference database | Session info

Quick Checklist | Naming & Organization | Documentation Standards | 1. @section Plot parameters not implemented or with altered functionality: | 2. @section Plot parameters and defaults: | 3. @section Plot parameters implementing new functionality: | Functionality & Non-Exposed Inputs | Example App Requirement | Testing Requirements | Implementing a New Plotting Function (e.g., piePlot) | Supporting Reactive Defaults | Updating Your Own Inputs From the Server | Inputs Rebuilt by renderUI() | Axis Limits | Debouncing Free-Text Inputs | Persisting Manual Layout Edits | Server | Key helpers (all in R/plot_helpers.R) | Integrating Statistical Testing (Stats Tab) | UI | Key helpers (all in R/stat_helper.R) | Gallery App and Figure Builder | Review Before Submitting | Style Guide | Input Labels | Select Inputs | Tooltips with tipify | Reuse Uniform Input Helpers | Imports: @importFrom Over :: | Additional Conventions | Styling and CSS Containment | Only ever style classes this package created | A dropdown or popover parented to needs its own marker class | Check that the rule matches what you think it does | Keep layout out of inline styles | Do not assume anything about the parent | Shipping a stylesheet | Verifying containment | Sanitizing User-Provided Expressions | safe_eval_filter(expr_text, data) | validate_expression(expr_text, col_names) | safe_resolve_adj_fxn(fn_name) | What counts as "allowed"?

Introduction | The Pattern | A Minimal Example | The UI | The Server | Putting It Together | Hiding Base Module Inputs | Driving Base Module Inputs From Your Wrapper | Automatically Preserving Manual Title/Legend/Annotation Edits | Best Practices

How It Works | The Pipeline | Using Custom Models in the App | Setting Defaults | Adding a Custom Model Backend | Backend Spec | Example: drc (Dose-Response Curves) | Example: mgcv (GAMs) | Where to Register Backends | How Extra Fields Flow Through | API Reference | Security

defaults: pre-filling inputs | Finding valid keys | Validation | Reactive defaults: driving inputs from app state | Why not update*Input() from the parent? | Passing defaults through createModuleApp() and *App() | hide.inputs: hiding individual controls | Use case: app-level fixed parameters | hide.tabs: hiding entire tab panels | Available tab names | Combining defaults, hide.inputs, and hide.tabs | Using hide.inputs in createModuleApp() and *App() | Hiding inputs dynamically in a custom module

Introduction | What the module does | Arguments | Return value | Showing fewer columns | A minimal example | Linking several modules to one table | How it compares to createModuleApp() | Summary

See the modules | Working with an AI coding agent | Drop a module into your app | Set defaults and hide controls | App factory with createModuleApp() | Export Summary Data | Which plot parameters are exposed?

Using the Stats tab | Supported tests | Paired tests | Adjusted, faceted and rotated axes | Downloading statistics | Using the stat helpers in a custom module | Restricting comparisons | Faceted plots and nested grouping | Test and draw on the plotted values | compute_pairwise_stats() return value

multiColorPicker | Overview | Basic Usage | Key Arguments | Reading the Value | Updating from the Server | Summary | multiDynamicInput | Defining Fields with row_spec | Pre-filled Rows with elements | Backend-Specific Fields | Writing Your Own Custom Input | Styling: the rule that matters most | Widgets that escape their container | Confirm your selectors actually match | Other practices worth copying

Introduction | Installation | 1. Download the package from Bioconductor | 2. Load the package into R session | Quick start: DESeq2 | Conduct principal component analysis (PCA): | A scree plot | A bi-plot | Quick start: Gene Expression Omnibus (GEO) | A pairs plot | A loadings plot | An eigencor plot | Access the internal data | Advanced features | Determine optimum number of PCs to retain | Modify bi-plots | Colour by a metadata factor, use a custom label, add lines through origin, and add legend | Supply custom colours and encircle variables by group | Stat ellipses | Change shape based on tumour grade, remove connectors, and add titles | Modify line types, remove gridlines, and increase point size | Colour by a continuous variable and plot other PCs | Quickly explore potentially informative PCs via a pairs plot | Determine the variables that drive variation among each PC | Correlate the principal components back to the clinical data | Plot the entire project on a single panel | Make predictions on new data | Acknowledgments | Session info | References

Introduction | Installation | Usage | MAGeCK MLE Output | The QC Tab | Highlighting Gene(sets) | The sgRNA Tab | The DepMap Tab

Introduction | Installation | 1. Download the package from Bioconductor | 2. Load the package into R session | Quick start | Plot the most basic volcano plot | Advanced features | Modify cut-offs for log2FC and P value; specify title; adjust point and label size | Adjust colour and alpha for point shading | Adjust shape of plotted points | Adjust cut-off lines and add extra threshold lines | Adjust legend position, size, and text | Fit more labels by adding connectors | Only label key variables | Draw labels in boxes | Italicise labels and flip volcano on it's side | Over-ride colouring scheme with custom key-value pairs | Over-ride colour and/or shape scheme with custom key-value pairs | Encircle / highlight certain variables | Highlighting key variables via custom point sizes | Change to continuous colour scheme | Custom axis tick marks | Acknowledgments | Session info | References