pepdiff: Differential Abundance Analysis for Phosphoproteomics Data

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.

Version:	1.0.0
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
Published:	2026-04-02
DOI:	10.32614/CRAN.package.pepdiff (may not be active yet)
Author:	Dan MacLean [aut, cre]
Maintainer:	Dan MacLean <dan.maclean at tsl.ac.uk>
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	pepdiff results

Documentation:

Reference manual:	pepdiff.html , pepdiff.pdf
Vignettes:	Non-parametric Factorial Analysis with ART (source, R code) Getting Started with pepdiff (source, R code) Checking GLM Model Fit (source, R code) Visual Quality Control and Interpretation (source, R code) Factorial Designs with GLM (source, R code) Two-Group Comparisons with Pairwise Tests (source, R code)

Downloads:

Package source:	pepdiff_1.0.0.tar.gz
Windows binaries:	r-devel: pepdiff_1.0.0.zip, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): pepdiff_1.0.0.tgz, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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