R Observatory: Metrics for pmartR version 2.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pmartR

2.5.1

Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

0packages depend

5.2Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Lisa BramerFirst published 2023-12-068 releasesCRAN page ↗GitHub ↗

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) doi:10.1074/mcp.M113.030932. Webb-Robertson et al. (2011) doi:10.1002/pmic.201100078. Matzke et al. (2011) doi:10.1093/bioinformatics/btr479. Matzke et al. (2013) doi:10.1002/pmic.201200269. Polpitiya et al. (2008) doi:10.1093/bioinformatics/btn217. Webb-Robertson et al. (2010) doi:10.1021/pr1005247.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("pmartR/pmartR")

Development version from pmartR/pmartR. Installs pak first if it is not already available.

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-pmartr

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 7.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.69

not tracked

Coverage

98%

Documentation · exports

19

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 710 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 10%

Downloads

5.2K

CRAN downloads in the past year

Rank #8,389 · ~14/day · ~436/mo

Releases R versions

Daily download trend is not available in this view yet.

36030 days

1.1K90 days

5.2K1 year

Compare downloads with other packages →

Also on417 r2u

Repository

GitHub ↗ pmartr/pmartr

48Stars

18Forks

10Open issues

2Open PRs

9Releases

1,476Commits

17Contributors

metabolomics-datapeptidesmass-spectrometrydata-summarizationproteinsmetaboliteslipidsrna-seq-analysis

1,476 commits · Last activity 2026-02-06 · 0% stars, 30d

Stars over time

2025-08-17 · 462026-07-07 · 48

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/pmartr/pmartr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (19)

Rcpp data.table doParallel dplyr ggplot2 e1071 foreachmethodsmvtnorm pcaMethods purrr rrcov stringr tidyr RColorBrewer magrittr parallelly patchwork glmpca

LinkingTo (3)

Rcpp RcppArmadillo BH

Suggests (13)

knitr limma rmarkdown edgeR DESeq2 plotly scales S4Vectorssurvivaltestthat trelliscopejs pmartRdata vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Lisa Bramer

Author, Maintainer

Authors (3)

Lisa Bramer

Author, Maintainer

Daniel Claborne

Author

Kelly Stratton

Author

Contributors (4)

Contributor

Contributor

Contributor

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.5.1Latest
2025-10-22 · current release · diff ↗
2.5.0
2025-04-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.4.6
2024-10-14 · diff ↗
2.4.5
2024-05-21 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.4.4
2024-02-27 · diff ↗
2.4.3
2024-02-27 · diff ↗
unarchivedReturned to CRAN
2024-02-27
archivedRemoved from CRAN
2024-02-27
policy violation Checking creates and leaves behind '~/Downloads'
2.4.2
2023-12-12 · diff ↗
2.4.1
2023-12-06
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-06
Total releases: 8 / 3 yrs
License: BSD_2_clause + file LICENSE OSI
Additional repositories: pmartR.github.io
Minimum R: ≥ 4.1.0
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pmartR")

Format

Bramer, L., Claborne, D., Degnan, D., Glasscock, E., Martin, E., Richardson, R., & Stratton, K. (2025). pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data (Version 2.5.1) [Computer software]. https://doi.org/10.32614/CRAN.package.pmartR

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 pmartR version 2.5.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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