protti

1.0.0

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

0packages depend

9.3Kdownloads / year

19.5%test coverage

13/13checks pass

Overview

About

Maintained by Jan-Philipp QuastFirst published 2021-04-2315 releasesCRAN page ↗GitHub ↗

Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) doi:10.1038/nbt.2999) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.

Install

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

install.packages("protti", 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("jpquast/protti")

Development version from jpquast/protti. 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-protti

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-protti

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-protti

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

Health

CRAN checks

13OK

Slowest check: 6.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.12

19.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 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
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,707 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 53%
Documented parameters: 99%
Return-value docs: 100%
References docs: 1%

Downloads

9.3K

CRAN downloads in the past year

Rank #4,233 · ~26/day · ~777/mo

Releases R versions

Daily download trend is not available in this view yet.

52830 days

2.2K90 days

9.3K1 year

Compare downloads with other packages →

Also on123 r2u37 autocran31 c2d4u

Repository

GitHub ↗ jpquast/protti

66Stars

9Forks

9Open issues

2Open PRs

15Releases

1,132Commits

7Contributors

rproteomicsmass-spectrometrydata-analysissystems-biologylip-msomicsprotein

1,132 commits · Last activity 2026-03-03 · 0% stars, 30d

Stars over time

2025-05-27 · 612026-07-07 · 66

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jpquast/protti on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

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

44 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (23)

rlang dplyr stringr magrittr data.table janitor progress purrr tidyr ggplot2 forcats tibble plotly ggrepelutilsgrDevicescurl readr lifecycle httrmethodsR.utilsstats

LinkingTo (0)

none

Suggests (26)

testthat covr knitr rmarkdown shiny r3dmol proDA limma dendextend pheatmap heatmaply furrr futureparallelseriation drc igraph stringi STRINGdb iq scales farver ggforce xml2 jsonlite missForest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Jan-Philipp Quast

Author, Maintainer

Authors (2)

Author, Maintainer

Author

Funders (1)

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-01-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.9.1
2024-10-22 · diff ↗
0.9.0
2024-07-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.8.0
2024-03-28 · diff ↗
0.7.0
2024-02-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.6.0
2023-01-20 · diff ↗
0.5.0
2022-09-29 · diff ↗
0.4.0
2022-09-08 · diff ↗
unarchivedReturned to CRAN
2022-09-08
archivedRemoved from CRAN
2022-09-04
issues were not corrected in time
0.3.1
2022-07-01 · diff ↗
R
R 4.2.0 released · 2022-04-22

Show 10 earlier events

0.3.0
2022-04-12 · diff ↗
0.2.2
2022-03-08 · diff ↗
unarchivedReturned to CRAN
2022-03-08
archivedRemoved from CRAN
2022-02-22
check problems were not corrected in time
0.2.1
2022-01-11 · diff ↗
0.2.0
2021-09-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.1
2021-05-10 · diff ↗
0.1.0
2021-04-23
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-23
Total releases: 15 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 327 KB / 9 files
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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