R Observatory: Metrics for biogram version 1.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

biogram

1.6.3

N-Gram Analysis of Biological Sequences

3packages depend

4.5Kdownloads / year

46.3%test coverage

0/13checks pass

Overview

About

Maintained by Michal BurdukiewiczFirst published 2014-12-197 releasesCRAN page ↗GitHub ↗

Tools for extraction and analysis of various n-grams (k-mers) derived from biological sequences (proteins or nucleic acids). Contains QuiPT (quick permutation test) for fast feature-filtering of the n-gram data.

Install

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

install.packages("biogram", 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("michbur/biogram")

Development version from michbur/biogram. 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-biogram

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-biogram

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-biogram

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

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

Code health

Yes

Tests · ratio 0.09

46.3%

Coverage · measured lines

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 98 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 99%
Return-value docs: 85%
References docs: 8%

Downloads

4.5K

CRAN downloads in the past year

Rank #10,594 · ~12/day · ~371/mo

Releases R versions

Daily download trend is not available in this view yet.

24430 days

93190 days

4.5K1 year

Compare downloads with other packages →

Also on165 r2u23 autocran

Repository

GitHub ↗ michbur/biogram

10Stars

1Forks

7Open issues

0Open PRs

3Releases

443Commits

6Contributors

biological-sequencesngram-analysisr

443 commits · Last activity 2026-07-07

Stars over time

2024-09-02 · 102026-07-07 · 10

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/michbur/biogram on 2026-08-09.

Continuous integration (1)

Travis CI

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0.0slam

Imports (3)

combinat entropy partitions

LinkingTo (0)

none

Suggests (3)

ggplot2 knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

AmpGram AmyloGram CancerGram

Code & Tests

People & History

People (5)

Maintainer (1)

Michal Burdukiewicz

Maintainer, Author

Authors (4)

Michal Burdukiewicz

Maintainer, Author

Chris Lauber

Author

Dominik Rafacz

Author · added in 1.6.1

Piotr Sobczyk

Author

Contributors (1)

Katarzyna Sidorczuk

Contributor · added in 1.6.3

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
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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.6.3Latest
2020-03-31 · current release · diff ↗
1.6.1
2020-01-09 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.4
2017-01-06 · diff ↗
1.3
2016-09-21 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.2
2015-06-22 · diff ↗

Show 4 earlier events

R
R 3.2.0 released · 2015-04-16
1.1
2015-02-03 · diff ↗
1.0
2014-12-19
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-12-19
Total releases: 7 / 12 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 67 KB / 2 files
Download size: 235 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biogram")

Format

Burdukiewicz, M., Lauber, C., Rafacz, D., Sidorczuk, K., & Sobczyk, P. (2020). biogram: N-Gram Analysis of Biological Sequences (Version 1.6.3) [Computer software]. https://doi.org/10.32614/CRAN.package.biogram

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 biogram version 1.6.3 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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