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

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) | Integrating Statistical Testing (Stats Tab) | UI | Server | Key helpers (all in R/stat_helper.R) | Gallery App | Review Before Submitting | Style Guide | Input Labels | Tooltips with tipify | Reuse Uniform Input Helpers | Imports: @importFrom Over :: | Additional Conventions | 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 | Best Practices | See Also

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