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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 
[aut, cre],
Richard Copley
[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:
Downloads:
Linking:
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https://CRAN.R-project.org/package=macrosyntR
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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.
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