{ "_id": "6a129c66acfb0bcc41d0f0d6", "Package": "macrosyntR", "Type": "Package", "Title": "Draw Ordered Oxford Grids", "Version": "0.3.4", "Authors@R": "c(person(given=\"Sami\",\nfamily =\"El Hilali\",\nemail = \"elhilali.sami@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4417-8399\")),\nperson(given=\"Richard\",\nfamily=\"Copley\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-7846-4954\"))\n)", "Maintainer": "Sami El Hilali ", "Description": "Use standard genomics file format (BED) and a table of\northologs to illustrate synteny conservation at the genome-wide\nscale. Significantly conserved linkage groups are identified as\ndescribed in Simakov et al. (2020)\n and displayed on an Oxford Grid\n(Edwards (1991) ) or a\nchord diagram as in Simakov et al. (2022)\n. The package provides a function\nthat uses a network-based greedy algorithm to find communities\n(Clauset et al. (2004) ) and so\nautomatically order the chromosomes on the plot to improve\ninterpretability.", "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", "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": { "Date": "2026-05-24 06:30:53 UTC", "User": "root" }, "Author": "Sami El Hilali [aut, cre] (ORCID:\n),\nRichard Copley [aut] (ORCID: )", "MD5sum": "c8b6cb9179203c201804b9368c8dea05", "_user": "samilhll", "_type": "src", "_file": "macrosyntR_0.3.4.tar.gz", "_fileid": "da80b9455e01c57f4b141e59a72adf03c9ed6bea7f1a3f32caa171d71866912b", "_filesize": 5515268, "_sha256": "da80b9455e01c57f4b141e59a72adf03c9ed6bea7f1a3f32caa171d71866912b", "_created": "2026-05-24T06:30:53.000Z", "_published": "2026-05-24T06:36:22.218Z", "_distro": "noble", "_jobs": [ { "job": 77577472093, "time": 151, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7182909200" }, { "job": 77577472096, "time": 139, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7182908047" }, { "job": 77577472101, "time": 295, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7182920946" }, { "job": 77577472097, "time": 175, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7182907693" }, { "job": 77577274998, "time": 233, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7182893424" }, { "job": 77577472079, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7182905312" }, { "job": 77577472091, "time": 116, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7182905667" }, { "job": 77577472092, "time": 96, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7182903765" }, { "job": 77577472087, "time": 92, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7182903414" } ], "_buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/samilhll/macrosyntr", "_commit": { "id": "a86189db19dafb15e78898e431f65df974618edc", "author": "Sami ", "committer": "Sami ", "message": "v0.3.4 introducing control over gap_size in plot_chord_diagram()\n", "time": 1717664125 }, "_maintainer": { "name": "Sami El Hilali", "email": "elhilali.sami@gmail.com", "login": "samilhll", "orcid": "0000-0003-4417-8399", "description": "Computational biologist specialized in genomics", "uuid": 37333782 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "samilhll", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "bioinformatics", "genomic-visualizations", "genomics" ], "_stars": 15, "_contributors": [ { "user": "samilhll", "count": 220, "uuid": 37333782 } ], "_userbio": { "uuid": 37333782, "type": "user", "name": "Sami El Hilali", "description": "Computational biologist specialized in genomics" }, "_downloads": { "count": 199, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/macrosyntR" }, "_devurl": "https://github.com/samilhll/macrosyntr", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/macrosyntR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/samilhll/macrosyntr", "_realowner": "samilhll", "_cranurl": true, "_releases": [ { "version": "0.2.14", "date": "2023-01-18" }, { "version": "0.2.19", "date": "2023-03-29" }, { "version": "0.3.3", "date": "2023-11-14" } ], "_exports": [ "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" ], "_help": [ { "page": "compute_linkage_groups", "title": "Compute Linkage groups", "topics": [ "compute_linkage_groups" ] }, { "page": "compute_macrosynteny", "title": "Compute significant macrosynteny blocks", "topics": [ "compute_macrosynteny" ] }, { "page": "get_syntenic_genes", "title": "get the syntenic genes as a table", "topics": [ "get_syntenic_genes" ] }, { "page": "load_orthologs", "title": "load orthologs with their genomic coordinates.", "topics": [ "load_orthologs" ] }, { "page": "plot_chord_diagram", "title": "plot the Macro-synteny as a chord diagram", "topics": [ "plot_chord_diagram" ] }, { "page": "plot_macrosynteny", "title": "Plot Macro-synteny", "topics": [ "plot_macrosynteny" ] }, { "page": "plot_oxford_grid", "title": "plot the Macro-synteny as an oxford grid.", "topics": [ "plot_oxford_grid" ] }, { "page": "reorder_macrosynteny", "title": "Reorder the mbh_df before plotting", "topics": [ "reorder_macrosynteny" ] }, { "page": "reorder_multiple_macrosyntenies", "title": "Reorder the chromosomes of two or more species before plotting", "topics": [ "reorder_multiple_macrosyntenies" ] }, { "page": "reverse_species_order", "title": "Reverse order of the species in an orthologs_df.", "topics": [ "reverse_species_order" ] }, { "page": "subset_linkage_orthologs", "title": "Subset Orthologs contained in conserved linkage groups", "topics": [ "subset_linkage_orthologs" ] } ], "_readme": "https://github.com/samilhll/macrosyntr/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "igraph", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "pillar", "pkgconfig", "plyr", "purrr", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "macrosyntR.Rmd", "filename": "macrosyntR.html", "title": "macrosyntR", "author": "Sami El Hilali", "engine": "knitr::rmarkdown", "headings": [ "Overview :", "Step-by-step tutorial :", "1 - Pre-processing :", "1.1 - Foreword :", "1.2 - Example using two species (rbhXpress) :", "1.3 - Example using 3 species (Orthofinder) :", "2 - Load the data :", "3 - Compute linkage groups :", "4 - Reorder chromosome levels to group the linkage groups in clusters :", "4.1 - Automatic reordering using a network-based greedy algorithm :", "4.2 - Manually reorder/subset the Chromosomes :", "5 - Plot directly with reordering the linkage groups and coloring :", "6 - Customize the plots :", "6.1 - customize the legend :", "6.2 - change the color palette :", "7 - Integrate additional information using colors :", "8 - plot a chord diagram :" ], "created": "2022-10-26 20:36:24", "modified": "2023-11-06 15:06:56", "commits": 26 } ], "_score": 4.8750612633917, "_indexed": true, "_nocasepkg": "macrosyntr", "_universes": [ "samilhll" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.4", "date": "2026-05-24T06:33:03.000Z", "distro": "noble", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "1b7b1b5b402fc9e48dd752d75b22510b60a2396c837a0ef30062446e89323dac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.6.0", "os": "linux", "version": "0.3.4", "date": "2026-05-24T06:32:53.000Z", "distro": "noble", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "ef53ecf58ae42ae2fa75bafbf25f866291a521d682d3a17106cccd24fc8d5663", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.5.3", "os": "mac", "version": "0.3.4", "date": "2026-05-24T06:33:37.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "a6479a06a586cdd2ed9304ee880a08be5a0282fb2876af51649fe71a2fe27664", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.6.0", "os": "mac", "version": "0.3.4", "date": "2026-05-24T06:32:58.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "2c8d46ea4bc34fdd2f91aea097a4554b406b41dc0662ef5c3d8b3b372ac279a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.4", "date": "2026-05-24T06:33:05.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "72656a76b0b3fea7bca94451870390150211d5a3fa25e98a0c59d127f08b6897", "status": "success", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.7.0", "os": "win", "version": "0.3.4", "date": "2026-05-24T06:32:16.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "7c6879641a1888bd38e3e27ec90de8e590d373cdfd42ed1fcfb782681fb8a937", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.5.3", "os": "win", "version": "0.3.4", "date": "2026-05-24T06:32:06.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "7410a44d91badd22dac329814e858bad761cdbd3bbeca224f6dd239d37a493c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" }, { "r": "4.6.0", "os": "win", "version": "0.3.4", "date": "2026-05-24T06:32:05.000Z", "commit": "a86189db19dafb15e78898e431f65df974618edc", "fileid": "4ec95ab3685bc769846f05ce6d116ffe0709bcba210ad338082e8a3d847b6dc4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samilhll/actions/runs/26353988538" } ] }