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

4packages dependsuggested by 1

19.5Kdownloads / year

68.3%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel OsorioCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4.6

READMEYes · 486 wordsVignettesNoNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites an R Journal article

Help pages: 33
Examples that run: 100%30 run in a plain check
Exported functions with examples: 97%
Documented parameters: 100%
Return-value docs: 74%
Help pages citing references: 79%

How these are measured

Downloads

19.5K

CRAN downloads in the past year

Rank #3,144 · ~54/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

3.9K90 days

19.5K1 year

Compare downloads with other packages →

Also on505 r2u7 autocran4.3K conda_forge66 c2d4u

How downloads are counted

Repository

dosorio/peptides ↗Account: dosorio

105Stars

24Forks

10Open issues

2Open PRs

11Releases

469Commits

11Commit identities

peptidesprotein-sequencescrancalculate-indicesbioinformaticsqsar

469 commits · Last activity 2023-12-13 · +1.9% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 72
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 1022026-10-14 · 105

How these are measured

PracticesBeta

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

Checks run against github.com/dosorio/peptides on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing Peptides adds 1 package (1 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB.

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Imports 4

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

AbSolution ampir pureseqtmr peptoolkit

Suggests, most downloaded first

AntibodyForests

How these are counted

Code & Tests

Datasets

People & History

People (7)

Daniel Osorio

Author, Maintainer since 0.1 (2014)

Paola Rondon-Villarreal

Author, Thesis advisor

Rodrigo Torres

Author, Thesis advisor · added in 2.0.0

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)

Show 3 peopleHide 3 people

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

Releases (23)

Pick two releases to compare their code metrics.

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
record
2023-12-13 · current release · diff ↗
2.4.5
record
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
record
2021-05-14 · diff ↗
2.4.3
record
2020-11-16 · diff ↗ ·
added 3 exports
aaSMILES, massShift, mz
2.4.2
record
2020-05-10 · diff ↗ ·
added 1 export
aaList
R
R 4.0.0 released · 2020-04-24
2.4.1
record
2019-08-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.4
record
2018-06-08 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 21 earlier eventsHide 21 earlier events

2.3
record
2018-03-18 · diff ↗
2.2
record
2017-06-06 · diff ↗
2.1
record
2017-05-03 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.0.0
record
2017-03-12 · diff ↗ ·
removed 5 exports
aacomp, aindex, instaindex, plot.xvg, read.xvg

added 14 exports
aIndex, aaComp, aaDescriptors, blosumIndices, fasgaiVectors, instaIndex, mswhimScores, plotXVG, protFP, readXVG, stScales, tScales, vhseScales, zScales
1.2.1
record
2017-02-21 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 18 exports
aacomp, aindex, autoCorrelation, autoCovariance, boman, charge, crossCovariance, crucianiProperties, hmoment, hydrophobicity, instaindex, kideraFactors, lengthpep, membpos, mw, pI, plot.xvg, read.xvg
1.1.2
record
2017-01-17 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1.1
record
2015-11-27 · diff ↗
1.1.0
record
2015-06-03 · diff ↗
1.0.4
record
2015-04-30 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0.3
record
2014-12-15 · diff ↗
1.0.2
record
2014-11-19 · diff ↗
1.0.1
record
2014-10-16 · diff ↗
1.0
record
2014-08-30 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.4
record
2014-03-26 · diff ↗
0.2
record
2014-02-22 · diff ↗
0.1
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("Peptides")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.32614/rj-2015-001.

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 v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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