maldipickr

1.3.3

Dereplicate and Cherry-Pick Mass Spectrometry Spectra

0packages depend

2.7Kdownloads / year

96.6%test coverage

13/13checks pass

Overview

About

Maintained by Charlie PauvertFirst published 2023-09-075 releasesCRAN page ↗GitHub ↗

Convenient wrapper functions for the analysis of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra data in order to select only representative spectra (also called cherry-pick). The package covers the preprocessing and dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik (2018) doi:10.3389/fmicb.2018.01294) needed to cluster MALDI-TOF spectra before the final cherry-picking step. It enables the easy exclusion of spectra and/or clusters to accommodate complex cherry-picking strategies. Alternatively, cherry-picking using taxonomic identification MALDI-TOF data is made easy with functions to import inconsistently formatted reports.

Install

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

install.packages("maldipickr", 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("ClavelLab/maldipickr")

Development version from ClavelLab/maldipickr. 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-maldipickr

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-maldipickr

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-maldipickr

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.51

96.6%

Coverage · measured lines

94%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 564 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 12%

Downloads

2.7K

CRAN downloads in the past year

Rank #11,620 · ~7/day · ~223/mo

Releases R versions

Daily download trend is not available in this view yet.

50130 days

91790 days

2.7K1 year

Compare downloads with other packages →

Also on107 r2u38 autocran

Repository

GitHub ↗ clavellab/maldipickr

3Stars

1Forks

5Open issues

0Open PRs

12Releases

283Commits

1Contributors

dereplicationmaldi-tof-mscherry-pickrr-packagesrstats

License GPL-3.0 · 283 commits · Last activity 2026-06-23 · 0% stars, 30d

Stars over time

2024-02-08 · 22026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/clavellab/maldipickr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

Zenodo

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.0

Imports (12)

dplyr lifecycle magrittr MALDIquant readBrukerFlexData rlangstatstibble tidyr tidyselecttoolsutils

LinkingTo (0)

none

Suggests (5)

coop knitr rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Charlie Pauvert

Author, Maintainer, Copyright holder

Authors (1)

Charlie Pauvert

Author, Maintainer, Copyright holder

Contributors (3)

Thomas Clavel

Contributor, Funder, Copyright holder

Selina Nüchtern

Contributor

David Wylensek

Contributor

Charlie Pauvert

Author, Maintainer, Copyright holder

Thomas Clavel

Contributor, Funder, Copyright holder

Funders (1)

Thomas Clavel

Contributor, Funder, Copyright holder

Package Timeline

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

1.3.3Latest
2026-06-23 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.1
2024-09-12 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.3.0
2023-12-14 · diff ↗
1.2.0
2023-10-25 · diff ↗
1.1.1
2023-09-07
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-07
Total releases: 5 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.2.0
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →