CRAN/E | rKOMICS

rKOMICS

Minicircle Sequence Classes (MSC) Analyses

Installation

About

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") *****.

Key Metrics

Version 1.3
R ≥ 2.10
Published 2023-06-29 463 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks rKOMICS results

Downloads

Yesterday 5 -55%
Last 7 days 45 -41%
Last 30 days 245 -3%
Last 90 days 699 +12%
Last 365 days 2.826 +15%

Maintainer

Maintainer

Manon Geerts

Authors

Frederik Van den Broeck

aut

Manon Geerts

aut / cre

Material

Reference manual
Package source

Vignettes

Application example

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

rKOMICS archive

Depends

R ≥ 2.10

Imports

ggplot2
ape
circlize
ComplexHeatmap
reshape2
utils
stats
dplyr
factoextra
FactoMineR
ggpubr
magrittr
stringr

Suggests

viridis