Why Check Model Fit? | Quick Check with plot_fit_diagnostics() | Reading the Diagnostic Plots | Panel A: Deviance Distribution | Panel B: Deviance vs Effect Size | Panel C: Sample Residual Plots | Panel D: Pooled QQ Plot | Investigating Flagged Peptides | Example: Data with Poor Fit | Decision: GLM or ART? | Use GLM when: | Consider ART when: | Try ART on the problematic data: | Summary

When you need GLM | Why Gamma GLM? | Example: 2×2 factorial design | The simulated peptide groups | What these patterns look like in raw data | Basic GLM analysis: main effects | Did GLM find the treatment effects? | Stratified comparisons with within | Stratified results by group | Handling interactions | When to use main effects vs stratified | Checking convergence | Model checking | Exporting results | Practical recommendations | Quick interaction check | When GLM struggles

What is pepdiff? | Installation | Setup | Creating example data | Importing data | Quick look at your data | Running a comparison | Understanding results | Getting significant hits | Visualising results | Comparing with our simulation | Next steps

What is ART? | When to consider ART | Example: 2×2 factorial design | The simulated peptide groups | What these patterns look like in raw data | Running ART analysis | Did ART find the treatment effects? | Stratified comparisons with within | Stratified results by group | Handling interactions | ART vs GLM comparison | Diagnostics | Exporting results | Limitations of ART | Practical recommendations | When both methods fail

When to use pairwise tests | Example data | The four pairwise tests | Wilcoxon rank-sum test | Bootstrap t-test | Bayes factor t-test | Rank products | How Rank Products differs from other tests | Comparing results across tests | FDR correction (p-value tests only) | Visualising results | Bayes factor plots | When pairwise isn't enough

Why visualise? | Creating example datasets | Data-level diagnostics | PCA plot | Distribution plots | Missingness plot | Results-level diagnostics | Volcano plot | P-value histogram | Fold change distribution | Individual plot functions | Exporting for publication | Summary: what to check

Citation | Simplest Use Case - Two Groups, No Replicates | Setting Options | Extended Use Case - Technical Replicates | Alternate Plot Options | Built-in Themes and Color Palettes | Theme Options | Color Palette Options | Quick Style Presets | Using besthr Palettes Directly | Styling Plots | Using Built-in Themes and Colors | Adding Titles and Annotations | Advanced Configuration | Using besthr_plot_config | Configuration Options | Building Custom Plots | Using besthr_data_view | Using Panel Builders | Alternative Visualizations | Raincloud Plots | Bootstrap Raincloud | CI Color Customization | Significance and Effect Size | Significance Annotations | Effect Size Annotation | Computing Statistics Directly | Summary Tables | Publication Export

Introduction | Installation | Setup | Generate Synthetic Pilot Data | Fit Distributions | Visualize Distribution Fits | Assess Fit Quality | A Note on Sample Size and Distribution Detection | Power Analysis - Aggregate Mode | Finding Required Sample Size | Finding Power at Fixed N | Power Analysis - Per-Peptide Mode | Interpreting Per-Peptide Results | Summary | Next Steps