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rKOMICS
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Download and install rKOMICS package within the R console
Install from CRAN:
install.packages("rKOMICS")
Install from Github:
library("remotes")
install_github("cran/rKOMICS")
Install by package version:
library("remotes")
install_version("rKOMICS", "1.3")
Attach the package and use:
library("rKOMICS")
Maintained by
Manon Geerts
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-02-17
Latest Update: 2023-06-29
Description:
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") *****.
How to cite:
Manon Geerts (2021). rKOMICS: Minicircle Sequence Classes (MSC) Analyses. R package version 1.3, https://cran.r-project.org/web/packages/rKOMICS
Previous versions and publish date:
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Other R packages that rKOMICS depends,
imports, suggests or enhances
Functions, R codes and Examples using
the rKOMICS R package
Some associated functions: exData . matrices . msc.depth . msc.heatmap . msc.length . msc.matrix . msc.pca . msc.quality . msc.richness . msc.seqs . msc.similarity . msc.subset . msc.uc . pipe . preprocess . rKOMICS . read.uc .
Some associated R codes: exData.R . matrices.R . msc.depth.R . msc.heatmap.R . msc.length.R . msc.matrix.R . msc.pca.R . msc.quality.R . msc.richness.R . msc.seqs.R . msc.similarity.R . msc.subset.R . msc.uc.R . preprocess.R . read.uc.R . utils-pipe.R . Full rKOMICS package functions and examples
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