Package: macrosyntR
Type: Package
Title: Draw Ordered Oxford Grids and Chord Diagrams
Version: 0.3.3
Authors@R: c(person(given="Sami",
 family ="El Hilali",
 email = "elhilali.sami@gmail.com",
 role = c("aut", "cre"),
 comment = c(ORCID = "0000-0003-4417-8399")),
 person(given="Richard",
 family="Copley",
 role = "aut",
 comment = c(ORCID = "0000-0001-7846-4954"))
  )
Maintainer: Sami El Hilali <elhilali.sami@gmail.com>
Depends: R (>= 4.1.0)
Imports: stats, utils, ggplot2, igraph, tidyr, reshape2, dplyr,
        stringr, rlang
Description: 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.
Encoding: UTF-8
License: GPL-3
URL: https://github.com/SamiLhll/macrosyntR
BugReports: https://github.com/SamiLhll/macrosyntR/issues
RoxygenNote: 7.2.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-14 15:05:34 UTC; sami
Author: Sami El Hilali [aut, cre] (<https://orcid.org/0000-0003-4417-8399>),
  Richard Copley [aut] (<https://orcid.org/0000-0001-7846-4954>)
Repository: CRAN
Date/Publication: 2023-11-14 16:40:02 UTC
Built: R 4.4.3; ; 2026-02-04 04:40:02 UTC; windows
