Package: macrosyntR 0.3.4

macrosyntR: Draw Ordered Oxford Grids

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.

Authors:Sami El Hilali [aut, cre], Richard Copley [aut]

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macrosyntR.pdf |macrosyntR.html
macrosyntR/json (API)
NEWS

# Install 'macrosyntR' in R:
install.packages('macrosyntR', repos = c('https://samilhll.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/samilhll/macrosyntr/issues

On CRAN:

Conda:

bioinformaticsgenomic-visualizationsgenomics

4.85 score 14 stars 5 scripts 194 downloads 11 exports 40 dependencies

Last updated 10 months agofrom:a86189db19. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 03 2025
R-4.5-winOKMar 03 2025
R-4.5-macOKMar 03 2025
R-4.5-linuxOKMar 03 2025
R-4.4-winOKMar 03 2025
R-4.4-macOKMar 03 2025
R-4.3-winOKMar 03 2025
R-4.3-macOKMar 03 2025

Exports:compute_linkage_groupscompute_macrosyntenyget_syntenic_genesload_orthologsplot_chord_diagramplot_macrosyntenyplot_oxford_gridreorder_macrosyntenyreorder_multiple_macrosynteniesreverse_species_ordersubset_linkage_orthologs

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

macrosyntR

Rendered frommacrosyntR.Rmdusingknitr::rmarkdownon Mar 03 2025.

Last update: 2023-11-06
Started: 2022-10-26