R Observatory: Metrics for PepMapViz version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PepMapViz

1.1.0Package record

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

0packages depend

2.7Kdownloads / year

40.9%test coverage

13/13flavors OK

Overview

About

Maintained by Zhenru ZhouCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 427 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 28
Examples that run: 96%27 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration HTML

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #16,784 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

33730 days

75790 days

2.7K1 year

Compare downloads with other packages →

Also on71 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing PepMapViz adds 62 packages (33 with compiled code, 63 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Zhenru Zhou

Author, Maintainer since 1.0.0 (2024)

Corey Bakalarski

Author

Qui Phung

Author

Listed in earlier versions (1)

Genentech, Inc.

no longer listed · 1.0.0

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-06-25 · current release · diff ↗ ·
added 3 exports
obtain_mod_mzIdenML, obtain_mod_mzTab, run_pepmap_app
R
R 4.5.0 released · 2025-04-11
1.0.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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