MALDIquant

1.22.3

Quantitative Analysis of Mass Spectrometry Data

5packages depend

79.3Kdownloads / year

88.7%test coverage

13/13checks pass

Overview

About

Maintained by Sebastian GibbFirst published 2011-02-2235 releasesCRAN page ↗GitHub ↗

A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

Install

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

install.packages("MALDIquant", 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("sgibb/MALDIquant")

Development version from sgibb/MALDIquant. 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-maldiquant

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-MALDIquant

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-MALDIquant

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

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.60

88.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 98%
Return-value docs: 100%
References docs: 17%

Downloads

79.3K

CRAN downloads in the past year

Rank #1,679 · ~217/day · ~6.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.1K30 days

16.3K90 days

79.3K1 year

Compare downloads with other packages →

Also on951 r2u240 autocran8.2K conda_forge418 bioconda85 c2d4u

Repository

GitHub ↗ sgibb/maldiquantArchived

68Stars

24Forks

2Open issues

3Open PRs

0Releases

654Commits

7Contributors

rmaldimass-spectrometryr-packagecranmaldi-tof-msmaldi-ims

654 commits · Last activity 2025-10-20 · 0% stars, 30d

Stars over time

2025-07-06 · 672026-07-07 · 68

Repository practices

Upstream repositoryBeta

Checks run against github.com/sgibb/maldiquant on 2026-07-19.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0.0methods

Imports (1)

parallel

LinkingTo (0)

none

Suggests (2)

knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

MALDIquantForeign MALDIrppa MSclassifR IsoCor maldipickr

Code & Tests

Code Composition

R 6,026 (60%)Rd 2,905 (29%)C 635 (6%)Vignettes 338 (3%)Other 61 (1%)

Code characteristics

Object systems

S4 class3S4 generic30S4 method49

Cyclomatic complexity: 1.0 median / 23 max
Test cases: 187 / 0.60 per code line

Test coverage

Line coverage

89%

Expression

90.7%

Tests / Examples

88.7% / 78% ex

Functions

112 20 exported

Complexity

2.4 avg / 23 max

Call network

112 nodes / 112 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

112 functions

Function	Cyclo	Coverage
.calculateLabelPositions	2	0%
.msiLegend	1	0%
.plotMsiSlice	11	0%
.rasterSlice	1	0%
.testLabelOverlap	4	0%
.which.closest	1	0%

People & History

People (5)

Maintainer (1)

Sebastian Gibb

Author, Maintainer

Authors (1)

Sebastian Gibb

Author, Maintainer

Contributors (3)

Laurent Gatto

Contributor · added in 1.21

Paolo Inglese

Contributor · added in 1.22

Sigurdur Smarason

Contributor · added in 1.21

Other (1)

Korbinian Strimmer

Thesis advisor · added in 1.3

Listed in earlier versions (1)

Paolo

no longer listed · 1.21

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.22.3Latest
2024-08-20 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.22.2
2024-01-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.22.1
2023-03-20 · diff ↗
1.22
2022-11-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.21
2021-12-23 · diff ↗
1.20
2021-07-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.19.3
2019-05-12 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.19.2
2019-03-13 · diff ↗

Show 37 earlier events

1.18
2018-07-06 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.17
2017-11-13 · diff ↗
1.16.4
2017-09-01 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.16.2
2017-04-04 · diff ↗
1.16.1
2017-01-11 · diff ↗
1.16
2016-12-14 · diff ↗
1.15
2016-06-25 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.14
2015-11-18 · diff ↗
1.13
2015-09-16 · diff ↗
1.12
2015-06-11 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.11
2014-08-11 · diff ↗
1.10
2014-04-11 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.9
2014-01-14 · diff ↗
1.8
2013-09-08 · diff ↗
1.7
2013-05-23 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.6
2013-03-01 · diff ↗
1.5
2012-12-07 · diff ↗
1.4
2012-10-30 · diff ↗
1.3
2012-09-16 · diff ↗
1.2
2012-07-18 · diff ↗
1.1
2012-05-06 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.0
2012-03-28 · diff ↗
0.5
2012-01-18 · diff ↗
R
R 2.14.0 released · 2011-10-31
0.4
2011-08-05 · diff ↗
0.3
2011-05-29 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.2
2011-03-29 · diff ↗
0.1
2011-02-22
R
R 2.12.0 released · 2010-10-15

Package metadata

First published: 2011-02-22
Total releases: 35 / 15 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0.0
Bundled data: 902 KB / 1 file
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Chemometrics and Computational Physics

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