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pepdiff  

Differential Abundance Analysis for Phosphoproteomics Data
View on CRAN: Click here


Download and install pepdiff package within the R console
Install from CRAN:
install.packages("pepdiff")

Install from Github:
library("remotes")
install_github("cran/pepdiff")

Install by package version:
library("remotes")
install_version("pepdiff", "1.0.0")



Attach the package and use:
library("pepdiff")
Maintained by
Dan MacLean
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-04-02
Latest Update: 2026-04-02
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.
How to cite:
Dan MacLean (2026). pepdiff: Differential Abundance Analysis for Phosphoproteomics Data. R package version 1.0.0, https://cran.r-project.org/web/packages/pepdiff. Accessed 21 Aug. 2026.
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