R Observatory: Metrics for pureseqtmr version 1.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pureseqtmr

1.4.2

Predict Transmembrane Protein Topology

0packages depend

3.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Richèl J.C. BilderbeekFirst published 2020-07-303 releasesCRAN page ↗GitHub ↗

Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (https://github.com/PureseqTM/pureseqTM_package, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), doi:10.1101/627307), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.

Install

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

install.packages("pureseqtmr", 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("richelbilderbeek/pureseqtmr")

Development version from richelbilderbeek/pureseqtmr. 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-pureseqtmr

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-pureseqtmr

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-pureseqtmr

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

Health

CRAN checks

13OK

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

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
OK2026-07-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 96%
Return-value docs: 93%
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #11,445 · ~11/day · ~324/mo

Releases R versions

Daily download trend is not available in this view yet.

17930 days

86090 days

3.9K1 year

Compare downloads with other packages →

Also on389 r2u18 autocran

Repository

GitHub ↗ richelbilderbeek/pureseqtmr

1Stars

2Forks

3Open issues

1Open PRs

10Releases

227Commits

2Contributors

License GPL-3.0 · 227 commits · Last activity 2026-07-04

Stars over time

2023-04-07 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/richelbilderbeek/pureseqtmr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (11)

data.table devtools dplyr ggplot2 Peptides plyr rappdirs readr stringr tibble Rcpp

LinkingTo (1)

Rcpp

Suggests (5)

testthat knitr markdown rmarkdown profvis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Authors (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

1.4.2Latest
2026-07-04 · current release · diff ↗
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
R
R 4.3.0 released · 2023-04-21
1.4
2023-04-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2
2020-07-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-30
Total releases: 3 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 255 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pureseqtmr")

Format

Bilderbeek, R. J. C. (2026). pureseqtmr: Predict Transmembrane Protein Topology (Version 1.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.pureseqtmr

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 pureseqtmr version 1.4.2 [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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