R Observatory: Metrics for kmeRtone version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

kmeRtone

1.0

Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

0packages depend

2Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Aleksandr SahakyanFirst published 2024-08-301 releasesCRAN page ↗GitHub ↗

A multi-purpose and flexible k-meric enrichment analysis software. 'kmeRtone' measures the enrichment of k-mers by comparing the population of k-mers in the case loci with a carefully devised internal negative control group, consisting of k-mers from regions close to, yet sufficiently distant from, the case loci to mitigate any potential sequencing bias. This method effectively captures both the local sequencing variations and broader sequence influences, while also correcting for potential biases, thereby ensuring more accurate analysis. The core functionality of 'kmeRtone' is the SCORE() function, which calculates the susceptibility scores for k-mers in case and control regions. Case regions are defined by the genomic coordinates provided in a file by the user and the control regions can be constructed relative to the case regions or provided directly. The k-meric susceptibility scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is highly flexible by allowing users to also specify their target k-mer patterns and quantify the corresponding k-mer enrichment scores in the context of these patterns, allowing for a more comprehensive approach to understanding the functional implications of specific DNA sequences on a genomic scale (e.g., CT motifs upon UV radiation damage). Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("kmeRtone", 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("SahakyanLab/kmeRtone")

Development version from SahakyanLab/kmeRtone. 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-kmertone

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-devel-windows-x86_64

Slowest check: 6.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

16

Dependencies · direct

Check history

ERROR2026-08-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-08-09
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
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

Show 12 earlier snapshots

OK2026-07-03
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-25
10 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE
OK2026-06-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-19
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
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
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-06
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 986 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 90%
References docs: 0%

Downloads

2K

CRAN downloads in the past year

Rank #16,890 · ~6/day · ~168/mo

Releases R versions

Daily download trend is not available in this view yet.

21630 days

65090 days

2K1 year

Compare downloads with other packages →

Also on385 r2u

Repository

GitHub ↗ sahakyanlab/kmertone

1Stars

0Forks

0Open issues

0Open PRs

1Releases

147Commits

5Contributors

License GPL-3.0 · 147 commits · Last activity 2025-04-14

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/sahakyanlab/kmertone on 2026-08-23.

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (16)

data.table R6 Rcpp R.utils openxlsx png RcppSimdJson venneuler stringi curl future future.apply jsonlite progressr Biostrings seqLogo

LinkingTo (2)

Rcpp stringi

Suggests (2)

rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Aleksandr Sahakyan

Author, Maintainer

Authors (3)

Aleksandr Sahakyan

Author, Maintainer

Adib Abdullah

Author

Patrick Pflughaupt

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-08-30
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2
Bundled data: 3.9 KB / 2 files
Download size: 915 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("kmeRtone")

Format

Sahakyan, A., Abdullah, A., & Pflughaupt, P. (2024). kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.kmeRtone

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 kmeRtone version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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