R Observatory: Metrics for ptm version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ptm

1.0.1

Analyses of Protein Post-Translational Modifications

0packages depend

4.1Kdownloads / year

76.7%test coverage

13/13checks pass

Overview

About

Maintained by Juan Carlos AledoFirst published 2020-12-167 releasesCRAN page ↗Bitbucket ↗

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins, with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download, filter and analyze data from the sulfoxidation database 'MetOSite'. Utilities to search and characterize S-aromatic motifs in proteins are also provided. In addition, functions to analyze sequence environments around modifiable residues in proteins can be found. For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable residues from the proteins of interest. Functions tailored to test statistical hypothesis related to these differential sequence environments are also implemented. Further and detailed information regarding the methods in this package can be found in (Aledo (2020) https://metositeptm.com).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("ptm", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-ptm

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-ptm

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.26

76.7%

Coverage · measured lines

100%

Documentation · exports

6

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 113 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 62%
Documented parameters: 94%
Return-value docs: 100%
References docs: 44%

Downloads

4.1K

CRAN downloads in the past year

Rank #9,785 · ~11/day · ~338/mo

Releases R versions

Daily download trend is not available in this view yet.

27430 days

97890 days

4.1K1 year

Compare downloads with other packages →

Also on130 r2u22 c2d4u

Repository

GitHub ↗ jcaledo/rptm

Repository practices

Upstream repositoryBeta

Repository github.com/jcaledo/rptm is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

bio3d curlgraphicshttr jsonlitestats

LinkingTo (0)

none

Suggests (3)

knitr markdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Juan Carlos Aledo

Author, Maintainer

Authors (1)

Juan Carlos Aledo

Author, Maintainer

Package Timeline

7 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
1.0.1Latest
2024-05-21 · current release · diff ↗
0.2.7
2024-05-09 · diff ↗
unarchivedReturned to CRAN
2024-05-09
archivedRemoved from CRAN
2024-05-04
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.6
2022-08-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.5
2022-02-14 · diff ↗
0.2.4
2021-05-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.3
2021-05-09 · diff ↗
0.2.2
2020-12-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-16
Total releases: 7 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 212 KB / 1 file
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ptm")

Format

Aledo, J. C. (2024). ptm: Analyses of Protein Post-Translational Modifications (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.ptm

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 ptm version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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