Package: pepdiff
Type: Package
Title: Differential Abundance Analysis for Phosphoproteomics Data
Version: 1.0.0
Author: Dan MacLean [aut, cre]
Description: 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.
Authors@R: person(given = "Dan", family = "MacLean", role = c("aut", "cre"), email = "dan.maclean@tsl.ac.uk")
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
biocViews:
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
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-03-30 12:23:29 UTC; macleand
Maintainer: Dan MacLean <dan.maclean@tsl.ac.uk>
Repository: CRAN
Date/Publication: 2026-04-02 20:00:02 UTC
Built: R 4.5.3; ; 2026-06-08 05:29:17 UTC; windows
