macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams

Use standard genomics file format (BED) and a table of orthologs to illustrate synteny conservation at the genome-wide scale. Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z> and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>. The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>) and so automatically order the chromosomes on the plot to improve interpretability.

Version:	0.3.3
Depends:	R (≥ 4.1.0)
Imports:	stats, utils, ggplot2, igraph, tidyr, reshape2, dplyr, stringr, rlang
Suggests:	knitr, rmarkdown
Published:	2023-11-14
DOI:	10.32614/CRAN.package.macrosyntR
Author:	Sami El Hilali [aut, cre], Richard Copley [aut]
Maintainer:	Sami El Hilali <elhilali.sami at gmail.com>
BugReports:	https://github.com/SamiLhll/macrosyntR/issues
License:	GPL-3
URL:	https://github.com/SamiLhll/macrosyntR
NeedsCompilation:	no
Citation:	macrosyntR citation info
Materials:	README NEWS
CRAN checks:	macrosyntR results

Documentation:

Reference manual:	macrosyntR.pdf
Vignettes:	macrosyntR

Downloads:

Package source:	macrosyntR_0.3.3.tar.gz
Windows binaries:	r-devel: macrosyntR_0.3.3.zip, r-release: macrosyntR_0.3.3.zip, r-oldrel: macrosyntR_0.3.3.zip
macOS binaries:	r-release (arm64): macrosyntR_0.3.3.tgz, r-oldrel (arm64): macrosyntR_0.3.3.tgz, r-release (x86_64): macrosyntR_0.3.3.tgz, r-oldrel (x86_64): macrosyntR_0.3.3.tgz
Old sources:	macrosyntR archive

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