R Observatory: Metrics for peptoolkit version 0.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

peptoolkit

0.0.1Package record

A Toolkit for Using Peptide Sequences in Machine Learning

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Josep-Ramon CodinaCRAN page ↗GitHub ↗Issues ↗

This toolkit is designed for manipulation and analysis of peptides. It provides functionalities to assist researchers in peptide engineering and proteomics. Users can manipulate peptides by adding amino acids at every position, count occurrences of each amino acid at each position, and transform amino acid counts based on probabilities. The package offers functionalities to select the best versus the worst peptides and analyze these peptides, which includes counting specific residues, reducing peptide sequences, extracting features through One Hot Encoding (OHE), and utilizing Quantitative Structure-Activity Relationship (QSAR) properties (based in the package 'Peptides' by Osorio et al. (2015) doi:10.32614/RJ-2015-001). This package is intended for both researchers and bioinformatics enthusiasts working on peptide-based projects, especially for their use with machine learning.

Install

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

install.packages("peptoolkit", 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("jrcodina/peptoolkit")

Development version from jrcodina/peptoolkit. 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-peptoolkit

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-peptoolkit

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-peptoolkit

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: 1.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.1

READMEYes · 217 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Description cites an R Journal article

Help pages: 8
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #23,728 · ~5/day · ~163/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

53490 days

2K1 year

Compare downloads with other packages →

Also on67 r2u1 autocran

How downloads are counted

Repository

jrcodina/peptoolkit ↗Account: jrcodina

0Stars

0Forks

0Open issues

0Open PRs

0Releases

License file reads as GPL-3.0 · Last activity 2023-09-26 · Default branch at 0.0.2, ahead of CRAN 0.0.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: not measured

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/jrcodina/peptoolkit on 2026-10-18.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing peptoolkit adds 64 packages (35 with compiled code, 49 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.3.0

Imports (5)

Peptidesstatsdplyr stringr caret

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Josep-Ramon Codina

Author, Maintainer since 0.0.1 (2023)

Releases (1)

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
0.0.1Latest
record
2023-07-13 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-13
Total releases: 1 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.3.0
Download size: 8.9 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("peptoolkit")

Format

Codina, J. (2023). peptoolkit: A Toolkit for Using Peptide Sequences in Machine Learning (Version 0.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.peptoolkit

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 peptoolkit version 0.0.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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