Package: macrosyntR
Type: Package
Title: Draw Ordered Oxford Grids
Version: 0.3.4
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
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev
Repository: https://samilhll.r-universe.dev
Date/Publication: 2024-06-06 08:55:25 UTC
RemoteUrl: https://github.com/samilhll/macrosyntr
RemoteRef: HEAD
RemoteSha: a86189db19dafb15e78898e431f65df974618edc
NeedsCompilation: no
Packaged: 2026-09-21 07:18:13 UTC; root
Author: Sami El Hilali [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4417-8399>),
  Richard Copley [aut] (ORCID: <https://orcid.org/0000-0001-7846-4954>)