R Observatory: Metrics for bioseq version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bioseq

0.1.5

A Toolbox for Manipulating Biological Sequences

2packages depend

8.2Kdownloads / year

95.3%test coverage

13/13checks pass

Overview

About

Maintained by Francois KeckFirst published 2020-07-275 releasesCRAN page ↗GitHub ↗

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) doi:10.1111/2041-210X.13490. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

Install

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

install.packages("bioseq", 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("fkeck/bioseq")

Development version from fkeck/bioseq. 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-bioseq

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-bioseq

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-bioseq

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.30

95.3%

Coverage · measured lines

100%

Documentation · exports

12

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-05-22
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 135 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 80%
References docs: 7%

Downloads

8.2K

CRAN downloads in the past year

Rank #5,555 · ~22/day · ~682/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

1.4K90 days

8.2K1 year

Compare downloads with other packages →

Also on1.5K r2u36 autocran878 conda_forge17 c2d4u

Repository

GitHub ↗ fkeck/bioseq

26Stars

3Forks

8Open issues

0Open PRs

5Releases

126Commits

3Contributors

License GPL-3.0 · 126 commits · Last activity 2025-09-30 · 0% stars, 30d

Stars over time

2025-07-22 · 232026-07-07 · 26

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fkeck/bioseq on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (12)

methodsvctrs tibble ape crayon dplyr pillar stringi stringr stringdist readr rlang

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

refdb tidysq

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Francois Keck

Author, Maintainer, Copyright holder

Authors (1)

Francois Keck

Author, Maintainer, Copyright holder

Copyright holders (1)

Francois Keck

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.5Latest
2025-09-29 · current release · diff ↗
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
0.1.4
2022-09-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.3
2021-09-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.2
2020-11-26 · diff ↗
0.1.1
2020-07-27
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-27
Total releases: 5 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Bundled data: 3.7 KB / 1 file
Download size: 691 KB
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("bioseq")

Format

Keck, F. (2025). bioseq: A Toolbox for Manipulating Biological Sequences (Version 0.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.bioseq

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 bioseq version 0.1.5 [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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