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.">

macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams (original) (raw)

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 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

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