Differential Abundance Analysis for Phosphoproteomics Data R package pepdiff version 1.0.0 Provides tools for analyzing differential abundance in proteomics experiments. Implements S3 classes for data management and supports Generalized Linear Models (GLM; Nelder and Wedderburn (1972) <doi:10.2307/2344614>), Aligned Rank Transform (ART; Wobbrock et al. (2011) <doi:10.1145/1978942.1978963>), and pairwise test methods for statistical analysis. Includes visualization functions for Principal Component Analysis (PCA), volcano plots, and heatmaps. Software Depends: R (>= 4.1.0) Imports: dplyr, tidyr, tibble, rlang, readr, ggplot2, cowplot, emmeans, ARTool, stats, magrittr, stringr, forcats, grid Suggests: ComplexHeatmap, UpSetR, RColorBrewer, viridis, circlize, factoextra, RankProd, MKinfer, testthat (>= 3.0.0), knitr, rmarkdown Dan MacLean <dan.maclean@tsl.ac.uk> Comprehensive R Archive Network (CRAN) Dan MacLean [aut, cre] MIT + file LICENSE (https://CRAN.R-project.org/package=pepdiff/LICENSE) 2026-04-02 application/tgz https://CRAN.R-project.org/package=pepdiff doi:10.32614/CRAN.package.pepdiff