R Observatory: Metrics for PepMapViz version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PepMapViz

1.1.0

A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

0packages depend

2.6Kdownloads / year

40.9%test coverage

13/13checks pass

Overview

About

Maintained by Zhenru ZhouFirst published 2024-11-132 releasesCRAN page ↗

A versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of 'PepMapViz' include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of Major histocompatibility complex-presented peptide clusters in different antibody regions predicting immunogenicity in antibody drug development.

Install

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

install.packages("PepMapViz", 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-pepmapviz

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-PepMapViz

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-PepMapViz

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

Health

CRAN checks

13OK

Slowest check: 3.5 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.19

40.9%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 427 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #18,008 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

14330 days

62390 days

2.6K1 year

Compare downloads with other packages →

Also on105 r2u27 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (9)

shiny ggplot2 stringr ggforce ggh4x ggnewscale data.table rlang DT

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat mzID MSnbase

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Zhenru Zhou

Author, Maintainer

Authors (3)

Zhenru Zhou

Author, Maintainer

Corey Bakalarski

Author

Qui Phung

Author

Listed in earlier versions (1)

Genentech, Inc.

no longer listed · 1.0.0

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-06-25 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-11-13
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-13
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Download size: 449 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PepMapViz")

Format

Zhou, Z., Bakalarski, C., & Phung, Q. (2025). PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PepMapViz

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for PepMapViz version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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