macrosyntR: Draw Ordered Oxford Grids

Use standard genomics file format (BED) and a table of orthologs to illustrate pair-wise 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>). 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: 0.2.19
Depends: R (≥ 4.1.0)
Imports: stats, utils, ggplot2, ggthemes, igraph, tidyr, reshape2, dplyr, stringr
Suggests: knitr, rmarkdown
Published: 2023-03-29
Author: Sami El Hilali ORCID iD [aut, cre], Richard Copley ORCID iD [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_0.2.19.tar.gz
Windows binaries: r-devel: macrosyntR_0.2.19.zip, r-release: macrosyntR_0.2.19.zip, r-oldrel: macrosyntR_0.2.19.zip
macOS binaries: r-release (arm64): macrosyntR_0.2.14.tgz, r-oldrel (arm64): macrosyntR_0.2.14.tgz, r-release (x86_64): macrosyntR_0.2.19.tgz, r-oldrel (x86_64): macrosyntR_0.2.19.tgz
Old sources: macrosyntR archive

Linking:

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