Changes in version 1.0.0 (2026-04-02)                  

Initial release of pepdiff for differential abundance analysis of PRM
proteomics data.

Features

Analysis Methods

  - compare() - Main analysis function supporting three methods:
    
      - GLM: Gamma GLM with emmeans for factorial designs (recommended)
      - ART: Aligned Rank Transform for non-parametric analysis
      - Pairwise: Direct two-group comparisons (Wilcoxon, bootstrap-t,
        Bayes factor, rank products)

  - Stratified comparisons with within parameter for analysing effects
    within factor levels

Data Management

  - read_pepdiff() - Import CSV data with flexible factor specification
  - combine_tech_reps() - Combine technical replicates before analysis
  - S3 classes pepdiff_data and pepdiff_results with print, summary, and
    plot methods

Diagnostics

  - plot_fit_diagnostics() - Four-panel diagnostic plot for assessing
    GLM model fit
  - Stored residuals and fitted values for post-hoc diagnostics
  - Convergence tracking for all fitted models

Visualization

  - plot() methods for both data and results objects
  - plot_volcano() - Volcano plots with customizable thresholds
  - plot_heatmap() - Heatmaps of significant peptides (requires
    ComplexHeatmap)
  - plot_pca() - PCA visualization of samples
  - plot_pvalue_hist() - P-value distribution histograms
  - plot_fc_distribution() - Fold change distributions
  - plot_missingness() - Missing data patterns
  - plot_distributions() - Abundance distributions by group

Companion Package

pepdiff is designed to work alongside peppwR:

  - peppwR: "How many samples do I need?" (power analysis)
  - pepdiff: "What's differentially abundant?" (analysis)