R Observatory: Metrics for Peptides version 2.4.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Peptides

2.4.6

Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

5packages depend

21.6Kdownloads / year

68.3%test coverage

13/13checks pass

Overview

About

Maintained by Daniel OsorioFirst published 2014-02-2023 releasesCRAN page ↗GitHub ↗

Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.

Install

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

install.packages("Peptides", 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("dosorio/Peptides")

Development version from dosorio/Peptides. 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-peptides

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-Peptides

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-Peptides

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

Health

CRAN checks

13OK

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

Code health

Yes

Tests · ratio 0.15

68.3%

Coverage · measured lines

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
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 · 486 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 74%
References docs: 79%

Downloads

21.6K

CRAN downloads in the past year

Rank #2,859 · ~59/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

5.1K90 days

21.6K1 year

Compare downloads with other packages →

Also on459 r2u19 autocran4.6K conda_forge31 c2d4u

Repository

GitHub ↗ dosorio/peptides

103Stars

24Forks

10Open issues

2Open PRs

11Releases

469Commits

11Contributors

peptidesprotein-sequencescrancalculate-indicesbioinformaticsqsar

469 commits · Last activity 2024-01-23 · +1% stars, 30d

Stars over time

2026-07-14 · 1022026-07-30 · 103

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

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

Continuous integration (1)

Travis CI

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

AbSolution ampir peptoolkit pureseqtmr AntibodyForests

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Daniel Osorio

Author, Maintainer

Authors (3)

Daniel Osorio

Author, Maintainer

Paola Rondon-Villarreal

Author, Thesis advisor

Rodrigo Torres

Author, Thesis advisor · added in 2.0.0

Contributors (4)

Richèl J.C. Bilderbeek

Contributor · added in 2.4.3

Luis Pedro Coelho

Contributor · added in 2.4.2

J. Sebastian Paez

Contributor · added in 2.0.0

Florian C. Sigloch

Contributor · added in 2.4.3

Listed in earlier versions (3)

Rodrigo Torres PhD.

no longer listed · 0.1 to 0.4

Rodrigo Torres.

no longer listed · 1.0 to 1.2.1

Richel Bilderbeek

no longer listed · 2.4.2

Package Timeline

23 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
R
R 4.4.0 released · 2024-04-24
2.4.6Latest
2023-12-13 · current release · diff ↗
2.4.5
2023-05-10 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.4.4
2021-05-14 · diff ↗
2.4.3
2020-11-16 · diff ↗
2.4.2
2020-05-10 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.4.1
2019-08-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.4
2018-06-08 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 21 earlier events

2.3
2018-03-18 · diff ↗
2.2
2017-06-06 · diff ↗
2.1
2017-05-03 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.0.0
2017-03-12 · diff ↗
1.2.1
2017-02-21 · diff ↗
1.1.2
2017-01-17 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1.1
2015-11-27 · diff ↗
1.1.0
2015-06-03 · diff ↗
1.0.4
2015-04-30 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0.3
2014-12-15 · diff ↗
1.0.2
2014-11-19 · diff ↗
1.0.1
2014-10-16 · diff ↗
1.0
2014-08-30 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.4
2014-03-26 · diff ↗
0.2
2014-02-22 · diff ↗
0.1
2014-02-20
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-02-20
Total releases: 23 / 12 yrs
License: GPL-2 OSI
Bundled data: 15 KB / 3 files
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Peptides")

Format

Osorio, D., Bilderbeek, R. J. C., Coelho, L. P., Paez, J. S., Rondon-Villarreal, P., Sigloch, F. C., & Torres, R. (2023). Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences (Version 2.4.6) [Computer software]. https://doi.org/10.32614/CRAN.package.Peptides

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 Peptides version 2.4.6 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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