R Observatory: Metrics for ptm version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ptm

1.0.1Package record

Analyses of Protein Post-Translational Modifications

0packages depend

4Kdownloads / year

76.7%test coverage

13/13flavors OK

Overview

About

Maintained by Juan Carlos AledoCRAN page ↗Bitbucket ↗Website ↗

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).

Changes in 1.0.1

The structure of the package has been substantially simplified reducing multiples third parties dependencies in order to gain in robustness and portability. The focus has been put on the posttranslational modification of methionine. The users interested in the original functionality (extended utilities) still can opt to download one of the older version of the package at https://bitbucket.org/jcaledo/ptm.

From NEWS.md in the release

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. 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-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

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 113 wordsVignettesNoNEWSYes · 67% structured · mentions 1.0.1Citation fileYes · cites a publicationWebsiteYes

Help pages: 16
Examples that run: 62%8 run in a plain check · 5 never run
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 44%

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #10,151 · ~11/day · ~333/mo

Releases R versions

Daily download trend is not available in this view yet.

36930 days

98290 days

4K1 year

Compare downloads with other packages →

Also on85 r2u43 c2d4u

How downloads are counted

Repository

jcaledo/rptm ↗

Responsiveness

not measured

How these are measured

PracticesBeta

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

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing ptm adds 10 packages (8 with compiled code, 6.3 MB of source tarballs). Heaviest: Rcpp 1.8 MB, bio3d 1.5 MB, openssl 1.1 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Juan Carlos Aledo

Author, Maintainer since 0.2.2 (2020)

Releases (7)

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
1.0.1Latest
record
2024-05-21 · current release · diff ↗ ·
removed 57 exports
abundance, ac.scan, acc.dssp, atom.dpx, bg.go, ddG.profile, ddG.ptm, dis.scan, dpx, env.Ztest, env.extract, env.matrices, env.plot, find.aaindex, foldx.assembly, foldx.mut, foldx.stab, get.area, get.go, gl.scan, hdfisher.go, id.features, id.mapping, imutant, kegg.uniprot, me.scan, mkdssp, msa, net.go, ni.scan and 27 more
unarchivedReturned to CRAN
2024-05-09
0.2.7
record
2024-05-09 · diff ↗
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
record
2022-08-07 · diff ↗ ·
removed 1 export
compute.dssp
R
R 4.2.0 released · 2022-04-22
0.2.5
record
2022-02-14 · diff ↗
0.2.4
record
2021-05-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.3
record
2021-05-09 · diff ↗ ·
removed 12 exports
ball, custom.aln, dist2closest, get.hssp, gorilla, list.hom, parse.hssp, pdb.pep, pdb.res, res.dist, shannon, site.type

added 5 exports
gracefully_fail, kegg.uniprot, pdb.uniprot, uniprot.kegg, uniprot.pdb
0.2.2
record
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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("ptm")

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

It points to 10.1093/bioinformatics/btab348.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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