The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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 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_0.3.3.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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=macrosyntR to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.