promor

0.2.3

Proteomics Data Analysis and Modeling Tools

0packages depend

3.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Chathurani RanathungeFirst published 2022-07-206 releasesCRAN page ↗GitHub ↗

A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) doi:10.1021/acs.jproteome.5b00981), differential expression analysis (Ritchie et. al. (2015) doi:10.1093/nar/gkv007), and machine learning-based modeling (Kuhn (2008) doi:10.18637/jss.v028.i05).

Install

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

install.packages("promor", 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("caranathunge/promor")

Development version from caranathunge/promor. 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-promor

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

13OK

Slowest check: 7.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.18

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-10
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE

Show 6 earlier snapshots

WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-08
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-04-04
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-03
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 471 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 100%
Return-value docs: 100%
References docs: 26%

Downloads

3.7K

CRAN downloads in the past year

Rank #9,866 · ~10/day · ~307/mo

Releases R versions

Daily download trend is not available in this view yet.

31530 days

1.1K90 days

3.7K1 year

Compare downloads with other packages →

Also on193 r2u

Repository

GitHub ↗ caranathunge/promor

16Stars

5Forks

2Open issues

0Open PRs

6Releases

440Commits

2Contributors

biomarkerslfqmodelingproteomicsdifferential-expressionmachine-learningmass-spectrometryr

License LGPL-2.1 · 440 commits · Last activity 2026-05-07

Stars over time

2025-05-21 · 162026-07-07 · 16

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/caranathunge/promor on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (15)

reshape2 ggplot2 ggrepel gridExtra limma statmod pcaMethods VIM missForest caret kernlab xgboost naivebayes viridis pROC

LinkingTo (0)

none

Suggests (4)

covr knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 4,999 (67%)Rd 2,168 (29%)Vignettes 180 (2%)Other 69 (1%)

Code characteristics

Cyclomatic complexity: 4.0 median / 15 max
Test cases: 18 / 0.18 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

28 23 exported

Complexity

4.4 avg / 15 max

Call network

28 nodes / 16 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Chathurani Ranathunge

Author, Maintainer, Copyright holder

Authors (1)

Chathurani Ranathunge

Author, Maintainer, Copyright holder

Chathurani Ranathunge

Author, Maintainer, Copyright holder

Package Timeline

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

0.2.3Latest
2026-05-07 · current release · diff ↗
unarchivedReturned to CRAN
2026-05-07
archivedRemoved from CRAN
2026-04-28
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
0.2.2
2025-11-11 · diff ↗
unarchivedReturned to CRAN
2025-11-11
archivedRemoved from CRAN
2025-11-10
check issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.1
2023-07-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.0
2023-01-17 · diff ↗
0.1.1
2022-11-01 · diff ↗
0.1.0
2022-07-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-20
Total releases: 6 / 4 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.5.0
Bundled data: 788 KB / 4 files
Download size: 3.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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