rKOMICS

1.3

Minicircle Sequence Classes (MSC) Analyses

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Manon GeertsFirst published 2021-02-174 releasesCRAN 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.

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

Health

CRAN checks

13OK

Slowest check: 7.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

93%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 6%

Downloads

2.8K

CRAN downloads in the past year

Rank #14,072 · ~8/day · ~237/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

75990 days

2.8K1 year

Compare downloads with other packages →

Also on114 r2u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (2)

Maintainer (1)

Manon Geerts

Author, Maintainer

Authors (2)

Manon Geerts

Author, Maintainer

Frederik Van den Broeck

Author

Package Timeline

4 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
1.3Latest
2023-06-30 · current release · diff ↗
1.2
2023-06-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1
2021-07-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →