{
  "_id": "6abba4c399f7aa8c6aa4763a",
  "Package": "syntenet",
  "Title": "Inference And Analysis Of Synteny Networks",
  "Version": "1.15.0",
  "Date": "2022-03-28",
  "Authors@R": "c(\nperson(given = \"Fabrício\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\")),\nperson(given = \"Tao\",\nfamily = \"Zhao\",\nrole = \"aut\",\nemail = \"tao.zhao@nwafu.edu.cn\",\ncomment = c(ORCID = \"0000-0001-7302-6445\")),\nperson(given = \"Kristian K\",\nfamily = \"Ullrich\",\nrole = \"aut\",\nemail = \"ullrich@evolbio.mpg.de\",\ncomment = c(ORCID = \"0000-0003-4308-9626\")),\nperson(given = \"Yves\",\nfamily = \"Van de Peer\",\nrole = \"aut\",\nemail = \"yves.vandepeer@psb.vib-ugent.be\",\ncomment = c(ORCID = \"0000-0003-4327-3730\"))\n)",
  "Description": "syntenet can be used to infer synteny networks from\nwhole-genome protein sequences and analyze them. Anchor pairs\nare detected with the MCScanX algorithm, which was ported to\nthis package with the Rcpp framework for R and C++ integration.\nAnchor pairs from synteny analyses are treated as an undirected\nunweighted graph (i.e., a synteny network), and users can\nperform: i. network clustering; ii. phylogenomic profiling (by\nidentifying which species contain which clusters) and; iii.\nmicrosynteny-based phylogeny reconstruction with maximum\nlikelihood.",
  "License": "GPL-3",
  "URL": "https://github.com/almeidasilvaf/syntenet",
  "BugReports": "https://support.bioconductor.org/t/syntenet",
  "biocViews": "Software, NetworkInference, FunctionalGenomics,\nComparativeGenomics, Phylogenetics, SystemsBiology,\nGraphAndNetwork, WholeGenome, Network",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "LazyData": "false",
  "Config/pak/sysreqs": "cmake libglpk-dev make libuv1-dev libxml2-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:33 UTC",
  "RemoteUrl": "https://github.com/bioc/syntenet",
  "RemoteRef": "HEAD",
  "RemoteSha": "aa99fce22a69842d931f07aaa5b538ea7015f588",
  "Packaged": {
    "Date": "2026-09-29 10:13:49 UTC",
    "User": "root"
  },
  "Author": "Fabrício Almeida-Silva [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5314-2964>),\nTao Zhao [aut] (ORCID: <https://orcid.org/0000-0001-7302-6445>),\nKristian K Ullrich [aut] (ORCID:\n<https://orcid.org/0000-0003-4308-9626>),\nYves Van de Peer [aut] (ORCID: <https://orcid.org/0000-0003-4327-3730>)",
  "Maintainer": "Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "syntenet_1.15.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6b65f310c8ca22da904be9d878b11cebf25646b4520bcf0376ef6f52953eb6cf",
  "_filesize": 2694062,
  "_sha256": "6b65f310c8ca22da904be9d878b11cebf25646b4520bcf0376ef6f52953eb6cf",
  "_expires": "2027-01-07T11:45:00.000Z",
  "_created": "2026-09-29T10:13:49.000Z",
  "_published": "2026-09-29T11:45:07.213Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053",
  "_status": "success",
  "_upstream": "https://github.com/bioc/syntenet",
  "_commit": {
    "id": "aa99fce22a69842d931f07aaa5b538ea7015f588",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381113
  },
  "_maintainer": {
    "name": "Fabrício Almeida-Silva",
    "email": "fabricio_almeidasilva@hotmail.com",
    "login": "almeidasilvaf",
    "bluesky": "@almeidasilvaf.bsky.social",
    "description": "Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.\nMember of the Bioconductor Community Advisory Board.",
    "uuid": 61153286,
    "orcid": "0000-0002-5314-2964"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 109359808774,
      "time": 215,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11027395021"
    },
    {
      "job": 109359808903,
      "time": 244,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11026003029"
    },
    {
      "job": 109359808931,
      "time": 538,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11027840846"
    },
    {
      "job": 109359808916,
      "time": 232,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11026137172"
    },
    {
      "job": 109359808949,
      "time": 381,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11027670455"
    },
    {
      "job": 109359809092,
      "time": 233,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11030193716"
    },
    {
      "job": 109359808917,
      "time": 620,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11030104908"
    },
    {
      "job": 109359808986,
      "time": 216,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11030817119"
    },
    {
      "job": 109359808935,
      "time": 605,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11030553307"
    },
    {
      "job": 109357908653,
      "time": 327,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11025957217"
    },
    {
      "job": 109359808714,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11026166907"
    },
    {
      "job": 109359808814,
      "time": 381,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11026951653"
    },
    {
      "job": 109359808994,
      "time": 291,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11025663985"
    },
    {
      "job": 109359808811,
      "time": 227,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11026251946"
    },
    {
      "job": 109359808829,
      "time": 344,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11027760354"
    },
    {
      "job": 109359808856,
      "time": 253,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11027101318"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "testthat",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggnetwork",
      "role": "Imports"
    },
    {
      "package": "intergraph",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "ggtree",
      "role": "Suggests"
    },
    {
      "package": "labdsv",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "xml2",
      "role": "Suggests"
    },
    {
      "package": "networkD3",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.15.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.14.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "networkinference",
    "functionalgenomics",
    "comparativegenomics",
    "phylogenetics",
    "systemsbiology",
    "graphandnetwork",
    "wholegenome",
    "network",
    "comparative-genomics",
    "evolutionary-genomics",
    "network-science",
    "phylogenomics",
    "synteny",
    "synteny-network",
    "cpp"
  ],
  "_stars": 43,
  "_contributors": [
    {
      "user": "almeidasilvaf",
      "count": 92,
      "uuid": 61153286
    },
    {
      "user": "kullrich",
      "count": 37,
      "uuid": 8100643
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 466,
    "source": "https://www.bioconductor.org/packages/stats/bioc/syntenet"
  },
  "_devurl": "https://github.com/almeidasilvaf/syntenet",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/syntenet.html"
  ],
  "_homeurl": "https://github.com/almeidasilvaf/syntenet",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "binarize_and_transpose",
    "check_input",
    "cluster_network",
    "collapse_bidirectional_hits",
    "collapse_protein_ids",
    "create_species_id_table",
    "diamond_is_installed",
    "export_sequences",
    "fasta2AAStringSetlist",
    "find_GS_clusters",
    "gff2GRangesList",
    "infer_microsynteny_phylogeny",
    "infer_syntenet",
    "interspecies_synteny",
    "intraspecies_synteny",
    "iqtree_is_installed",
    "iqtree_version",
    "last_is_installed",
    "make_bidirectional",
    "parse_collinearity",
    "phylogenomic_profile",
    "plot_network",
    "plot_profiles",
    "process_input",
    "profiles2phylip",
    "rcpp_mcscanx_file",
    "read_diamond",
    "run_diamond",
    "run_last"
  ],
  "_datasets": [
    {
      "name": "angiosperm_phylogeny",
      "title": "Microsynteny-based angiosperm phylogeny.",
      "object": "angiosperm_phylogeny",
      "file": "angiosperm_phylogeny.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "annotation",
      "title": "Filtered genome annotation for Ostreococcus sp. species",
      "object": "annotation",
      "file": "annotation.rda",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blast_list",
      "title": "List of data frames containing BLAST-like tabular output",
      "object": "blast_list",
      "file": "blast_list.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "clusters",
      "title": "Synteny network clusters of BUSCO genes for 25 eudicot species",
      "object": "clusters",
      "file": "clusters.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene",
        "Cluster"
      ],
      "rows": 32653,
      "table": true,
      "tojson": true
    },
    {
      "name": "edges",
      "title": "Synteny network of Ostreococcus genomes represented as an edge list",
      "object": "edges",
      "file": "edges.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Anchor1",
        "Anchor2"
      ],
      "rows": 1064,
      "table": true,
      "tojson": true
    },
    {
      "name": "network",
      "title": "Synteny network of BUSCO genes for 25 eudicot species",
      "object": "network",
      "file": "network.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "node1",
        "node2"
      ],
      "rows": 226677,
      "table": true,
      "tojson": true
    },
    {
      "name": "proteomes",
      "title": "Filtered proteomes of Ostreococcus sp. species",
      "object": "proteomes",
      "file": "proteomes.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "scerevisiae_annot",
      "title": "Genome annotation of the yeast species S. cerevisiae",
      "object": "scerevisiae_annot",
      "file": "scerevisiae_annot.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "scerevisiae_diamond",
      "title": "Intraspecies DIAMOND output for S. cerevisiae",
      "object": "scerevisiae_diamond",
      "file": "scerevisiae_diamond.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "angiosperm_phylogeny",
      "title": "Microsynteny-based angiosperm phylogeny.",
      "topics": [
        "angiosperm_phylogeny"
      ]
    },
    {
      "page": "annotation",
      "title": "Filtered genome annotation for Ostreococcus sp. species",
      "topics": [
        "annotation"
      ]
    },
    {
      "page": "binarize_and_transpose",
      "title": "Binarize and transpose the phylogenomic profile matrix",
      "topics": [
        "binarize_and_transpose"
      ]
    },
    {
      "page": "blast_list",
      "title": "List of data frames containing BLAST-like tabular output",
      "topics": [
        "blast_list"
      ]
    },
    {
      "page": "check_input",
      "title": "Check if input objects are ready for further analyses",
      "topics": [
        "check_input"
      ]
    },
    {
      "page": "cluster_network",
      "title": "Cluster the synteny network using the Infomap algorithm",
      "topics": [
        "cluster_network"
      ]
    },
    {
      "page": "clusters",
      "title": "Synteny network clusters of BUSCO genes for 25 eudicot species",
      "topics": [
        "clusters"
      ]
    },
    {
      "page": "collapse_bidirectional_hits",
      "title": "Collapse a list of bidirectional DIAMOND hits",
      "topics": [
        "collapse_bidirectional_hits"
      ]
    },
    {
      "page": "collapse_protein_ids",
      "title": "Collapse protein IDs into gene IDs in sequence names of AAStringSet objects",
      "topics": [
        "collapse_protein_ids"
      ]
    },
    {
      "page": "create_species_id_table",
      "title": "Create a data frame of species IDs (3-5-character abbreviations)",
      "topics": [
        "create_species_id_table"
      ]
    },
    {
      "page": "diamond_is_installed",
      "title": "Check if DIAMOND is installed",
      "topics": [
        "diamond_is_installed"
      ]
    },
    {
      "page": "edges",
      "title": "Synteny network of Ostreococcus genomes represented as an edge list",
      "topics": [
        "edges"
      ]
    },
    {
      "page": "export_sequences",
      "title": "Export processed sequences as FASTA files",
      "topics": [
        "export_sequences"
      ]
    },
    {
      "page": "fasta2AAStringSetlist",
      "title": "Read FASTA files in a directory as a list of AAStringSet objects",
      "topics": [
        "fasta2AAStringSetlist"
      ]
    },
    {
      "page": "find_GS_clusters",
      "title": "Find group-specific clusters based on user-defined species classification",
      "topics": [
        "find_GS_clusters"
      ]
    },
    {
      "page": "gff2GRangesList",
      "title": "Read GFF/GTF files in a directory as a GRangesList object",
      "topics": [
        "gff2GRangesList"
      ]
    },
    {
      "page": "infer_microsynteny_phylogeny",
      "title": "Infer microsynteny-based phylogeny with IQTREE",
      "topics": [
        "infer_microsynteny_phylogeny"
      ]
    },
    {
      "page": "infer_syntenet",
      "title": "Infer synteny network",
      "topics": [
        "infer_syntenet"
      ]
    },
    {
      "page": "interspecies_synteny",
      "title": "Detect interspecies synteny",
      "topics": [
        "interspecies_synteny"
      ]
    },
    {
      "page": "intraspecies_synteny",
      "title": "Detect intraspecies synteny",
      "topics": [
        "intraspecies_synteny"
      ]
    },
    {
      "page": "iqtree_is_installed",
      "title": "Check if IQTREE is installed",
      "topics": [
        "iqtree_is_installed"
      ]
    },
    {
      "page": "iqtree_version",
      "title": "Get IQ-TREE version",
      "topics": [
        "iqtree_version"
      ]
    },
    {
      "page": "last_is_installed",
      "title": "Check if last is installed",
      "topics": [
        "last_is_installed"
      ]
    },
    {
      "page": "make_bidirectional",
      "title": "Create a data frame of bidirectional comparisons from unidirectional comparisons",
      "topics": [
        "make_bidirectional"
      ]
    },
    {
      "page": "network",
      "title": "Synteny network of BUSCO genes for 25 eudicot species",
      "topics": [
        "network"
      ]
    },
    {
      "page": "parse_collinearity",
      "title": "Parse .collinearity files obtained with MCScan",
      "topics": [
        "parse_collinearity"
      ]
    },
    {
      "page": "phylogenomic_profile",
      "title": "Perform phylogenomic profiling for synteny network clusters",
      "topics": [
        "phylogenomic_profile"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot network",
      "topics": [
        "plot_network"
      ]
    },
    {
      "page": "plot_profiles",
      "title": "Plot a heatmap of phylogenomic profiles",
      "topics": [
        "plot_profiles"
      ]
    },
    {
      "page": "process_input",
      "title": "Process sequence data",
      "topics": [
        "process_input"
      ]
    },
    {
      "page": "profiles2phylip",
      "title": "Save the transposed binary profiles matrix to a file in PHYLIP format",
      "topics": [
        "profiles2phylip"
      ]
    },
    {
      "page": "proteomes",
      "title": "Filtered proteomes of Ostreococcus sp. species",
      "topics": [
        "proteomes"
      ]
    },
    {
      "page": "rcpp_mcscanx_file",
      "title": "rcpp_mcscanx_file",
      "topics": [
        "rcpp_mcscanx_file"
      ]
    },
    {
      "page": "read_diamond",
      "title": "Read DIAMOND/BLAST tables as a list of data frames",
      "topics": [
        "read_diamond"
      ]
    },
    {
      "page": "run_diamond",
      "title": "Wrapper to run DIAMOND from an R session",
      "topics": [
        "run_diamond"
      ]
    },
    {
      "page": "run_last",
      "title": "Wrapper to run last from an R session",
      "topics": [
        "run_last"
      ]
    },
    {
      "page": "scerevisiae_annot",
      "title": "Genome annotation of the yeast species S. cerevisiae",
      "topics": [
        "scerevisiae_annot"
      ]
    },
    {
      "page": "scerevisiae_diamond",
      "title": "Intraspecies DIAMOND output for S. cerevisiae",
      "topics": [
        "scerevisiae_diamond"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/syntenet/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/syntenet/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "brio",
    "callr",
    "cli",
    "coda",
    "codetools",
    "cpp11",
    "crayon",
    "desc",
    "diffobj",
    "evaluate",
    "farver",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggnetwork",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "igraph",
    "intergraph",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "network",
    "otel",
    "pheatmap",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "pkgload",
    "praise",
    "processx",
    "ps",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rprojroot",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "sna",
    "snow",
    "statnet.common",
    "testthat",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite",
    "waldo",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "vignette_01_inference_and_analysis_of_synteny_networks.Rmd",
      "filename": "vignette_01_inference_and_analysis_of_synteny_networks.html",
      "title": "Inference and analysis of synteny networks",
      "author": "Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, Yves Van de Peer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Data description",
        "Importing data to the R session",
        "From FASTA files to a list of AAStringSet objects",
        "From GFF/GTF files to a GRangesList object",
        "Data preprocessing",
        "Synteny network inference",
        "Phylogenomic profiling",
        "Microsynteny-based phylogeny reconstruction",
        "FAQ",
        "How do I execute an external dependency that is not in my PATH?",
        "Can I run the DIAMOND searches on the command line and import the results?",
        "My sequence names do not match gene IDs in the annotation. What should I do?",
        "Session information",
        "References"
      ],
      "created": "2025-07-23 11:24:47",
      "modified": "2025-07-23 11:24:47",
      "commits": 1
    },
    {
      "source": "vignette_02_synteny_detection_with_syntenet.Rmd",
      "filename": "vignette_02_synteny_detection_with_syntenet.html",
      "title": "syntenet as a synteny detection tool",
      "author": "Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, Yves Van de Peer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Detecting intragenome synteny",
        "Detecting intergenome synteny",
        "Session information",
        "References"
      ],
      "created": "2025-07-23 11:24:47",
      "modified": "2025-07-23 11:24:47",
      "commits": 1
    }
  ],
  "_score": 6.712649701627212,
  "_indexed": true,
  "_nocasepkg": "syntenet",
  "_universes": [
    "bioc",
    "almeidasilvaf"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-09-29T10:17:00.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/17213dfbeae5cf527c815e9ab6ae5856b27dbcc88c5c9b5e7c74449564299d24",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-09-29T10:22:02.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/c49f720ea99db92655f5cd811cfeacd30c32f048ae0e4fc4448092a070918b66",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-09-29T10:16:59.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/2d1d4b1f396f6ae410ec07591cf57d5651cfdc1d433cc99bf3b4e2fd284ec03e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-09-29T10:19:00.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/921cd31e0e1e4040c1cf20d5ce5db7b32b7c1f504799778e1565d6fcf6917378",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-09-29T11:34:37.000Z",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/27c238e593e08802f7e565d37b18581cde5fcd8fd8d04f19c2bbe8ac51dc4394",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-09-29T11:38:35.000Z",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/1a241453270fc8e9cdba5ccc33ec35168bcd80c7642e50e8af6dff88aeebeb11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-09-29T11:34:46.000Z",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/fa9cbf8d2c96b9d72903ce7babc603e85670d365e694b306aea415660eb377df",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-09-29T11:37:37.000Z",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/011bae6bca47fa0bc61dfcb86046ce331d82093dd3fab0b48b72d352b9ac3f9a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.15.0",
      "date": "2026-09-29T10:17:16.000Z",
      "arch": "emscripten",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/728dbf93158df32443ad8548c5f8427f624ae983caf01ceb9f501e091fd3d721",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-09-29T10:18:38.000Z",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/b101bdfca15054243e2a99d40de9eb726ae5ab37773f877abfbec12f1f80bca9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-09-29T10:15:50.000Z",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/152d88402a6bfe202876df51bbd63c2cc7665d3a3782634e74715f584318a03d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-09-29T10:15:46.000Z",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/9403573fbfb93416bb068b23ba9dd9c0ac7d27391dd7a8a51173d56489e87807",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-09-29T10:18:15.000Z",
      "arch": "aarch64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/11736037d14e919ec6fe2c741e9d0c9a001e9d722a7febb20467c9eb017272a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-09-29T10:16:02.000Z",
      "arch": "x86_64",
      "commit": "aa99fce22a69842d931f07aaa5b538ea7015f588",
      "fileid": "https://r2.ropensci.org/c1f6682a37f86435013d75e3777c4ae4c01da4a53ba521100bac1396293a9c77",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36553667053"
    }
  ]
}