R Observatory: Metrics for rKOMICS version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rKOMICS

1.3Package record

Minicircle Sequence Classes (MSC) Analyses

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Manon GeertsCRAN page ↗

This is a analysis toolkit to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history. ***** !! WARNING: this package relies on dependencies from Bioconductor. For Mac users, this can generate errors when installing rKOMICS. Install Bioconductor and ComplexHeatmap at advance: install.packages("BiocManager"); BiocManager::install("ComplexHeatmap") *****.

Install

R (CRAN)Ubuntu (r2u)

install.packages("rKOMICS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-rkomics

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 17 (1 internal)includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 6%

Vignettes (1)

Application example PDF

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #16,385 · ~8/day · ~246/mo

Releases R versions

Daily download trend is not available in this view yet.

26130 days

77090 days

2.9K1 year

Compare downloads with other packages →

Also on76 r2u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing rKOMICS adds 118 packages (57 with compiled code, 111 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 2.10

Imports (13)

ggplot2 ape circlize ComplexHeatmap reshape2utilsstatsdplyr factoextra FactoMineR ggpubr magrittr stringr

LinkingTo (0)

none

Suggests (1)

viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Manon Geerts

Author, Maintainer since 1.0 (2021)

Frederik Van den Broeck

Author

Releases (4)

Pick two releases to compare their code metrics.

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
1.3Latest
record
2023-06-30 · current release · diff ↗
1.2
record
2023-06-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1
record
2021-07-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0
record
2021-02-17
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-17
Total releases: 4 / 5 yrs
License: GPL
Minimum R: ≥ 2.10
Bundled data: 58 KB / 2 files
Download size: 5.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rKOMICS")

Format

Geerts, M., & Van den Broeck, F. (2023). rKOMICS: Minicircle Sequence Classes (MSC) Analyses (Version 1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.rKOMICS

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 rKOMICS version 1.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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