pepdiff

1.0.0

Differential Abundance Analysis for Phosphoproteomics Data

0packages depend

805downloads / year

69.4%test coverage

13/13checks pass

Overview

About

Maintained by Dan MacLeanFirst published 2026-04-031 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("pepdiff", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pepdiff

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-pepdiff

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.90

69.4%

Coverage · measured lines

98%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-03
3 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 228 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 89%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

805

CRAN downloads in the past year

Rank #19,273 · ~2/day · ~67/mo

Releases R versions

Daily download trend is not available in this view yet.

17530 days

60090 days

8051 year

Compare downloads with other packages →

Also on25 r2u11 autocran

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (14)

dplyr tidyr tibble rlang readr ggplot2 cowplot emmeans ARToolstatsmagrittr stringr forcatsgrid

LinkingTo (0)

none

Suggests (11)

ComplexHeatmap UpSetR RColorBrewer viridis circlize factoextra RankProd MKinfer testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Dan MacLean

Author, Maintainer

Authors (1)

Dan MacLean

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-04-03 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-03
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →