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macrosyntR
View on CRAN: Click
here
Download and install macrosyntR package within the R console
Install from CRAN:
install.packages("macrosyntR")
Install from Github:
library("remotes")
install_github("cran/macrosyntR")
Install by package version:
library("remotes")
install_version("macrosyntR", "0.3.3")
Attach the package and use:
library("macrosyntR")
Maintained by
Sami El Hilali
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-01-18
Latest Update: 2023-11-14
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)
and displayed on an Oxford Grid (Edwards (1991) ) or a chord diagram as in Simakov et al. (2022) .
The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) )
and so automatically order the chromosomes on the plot to improve interpretability.
How to cite:
Sami El Hilali (2023). macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams. R package version 0.3.3, https://cran.r-project.org/web/packages/macrosyntR. Accessed 30 Jan. 2025.
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Other R packages that macrosyntR depends,
imports, suggests or enhances
Complete documentation for macrosyntR
Functions, R codes and Examples using
the macrosyntR R package
Some associated functions: compute_linkage_groups . compute_macrosynteny . get_syntenic_genes . load_orthologs . plot_chord_diagram . plot_macrosynteny . plot_oxford_grid . reorder_macrosynteny . reorder_multiple_macrosyntenies . reverse_species_order . subset_linkage_orthologs .
Some associated R codes: compute_linkage_groups.R . compute_macrosynteny.R . get_ideograms_coordinates.R . get_syntenic_genes.R . load_orthologs.R . plot_chord_diagram.R . plot_macrosynteny.R . plot_oxford_grid.R . reorder_macrosynteny.R . reorder_multiple_macrosyntenies.R . reverse_species_order.R . subset_linkage_orthologs.R . Full macrosyntR package functions and examples
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