tidysq

1.2.3

Tidy Processing and Analysis of Biological Sequences

0packages depend

3.3Kdownloads / year

90.7%test coverage

11/13checks pass

Overview

About

Maintained by Dominik RafaczFirst published 2021-03-126 releasesCRAN page ↗GitHub ↗

A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.

Install

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

install.packages("tidysq", 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("BioGenies/tidysq")

Development version from BioGenies/tidysq. 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-tidysq

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-tidysq

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-tidysq

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.78

90.7%

Coverage · measured lines

98%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 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
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 168 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #12,994 · ~9/day · ~275/mo

Releases R versions

Daily download trend is not available in this view yet.

24230 days

78690 days

3.3K1 year

Compare downloads with other packages →

Also on409 r2u5 autocran

Repository

GitHub ↗ biogenies/tidysq

44Stars

2Forks

52Open issues

0Open PRs

5Releases

1,527Commits

11Contributors

biological-sequencesrstatsbioinformaticstidyversertidybioconductorfasta

1,527 commits · Last activity 2025-01-08 · 0% stars, 30d

Stars over time

2025-06-10 · 432026-07-07 · 44

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/biogenies/tidysq on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Coverage (1)

Codecov

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (8)

checkmate cli crayon dplyr pillar Rcpp tibble (>= 2.1.3)vctrs

LinkingTo (2)

Rcpp testthat

Suggests (14)

ape bioseq Biostrings covr knitr lifecycle purrr seqinr spelling rmarkdown testthat withr rlang mockr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (10)

Maintainer (1)

Dominik Rafacz

Maintainer, Author

Authors (3)

Dominik Rafacz

Maintainer, Author

Laura Bakala

Author · added in 1.1.3

Michal Burdukiewicz

Author

Contributors (7)

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Listed in earlier versions (1)

Mateusz Bakala

no longer listed · 1.1.0 to 1.1.2-1

Package Timeline

6 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
1.2.3Latest
2025-01-07 · current release · diff ↗
1.2.2
2024-10-24 · diff ↗
1.2.1
2024-10-07 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1.3
2022-01-31 · diff ↗
unarchivedReturned to CRAN
2022-01-31
archivedRemoved from CRAN
2022-01-23
check problems were not corrected in time
1.1.2-1
2021-07-27 · diff ↗
unarchivedReturned to CRAN
2021-07-27
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2021-04-15
check problems were not corrected in time
1.1.0
2021-03-12

Show 1 earlier events

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-12
Total releases: 6 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.0
Download size: 193 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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