{
  "_id": "6acf33efd9de2f3f33fc9145",
  "Package": "orthGS",
  "Title": "Orthology vs Paralogy Relationships among Glutamine Synthetase\nfrom Plants",
  "Version": "0.1.8",
  "Authors@R": "c(\nperson(\"Elena\", \"Aledo\",  email = \"elenaaledoesteban@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Juan-Carlos\", \"Aledo\",  email = \"caledo@uma.es\", role = \"aut\", comment = c(ORCID = \"0000-0002-3497-9945\")))",
  "Description": "Tools to analyze and infer orthology and paralogy\nrelationships between glutamine synthetase proteins in seed\nplants.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 07:40:48 UTC",
    "User": "root"
  },
  "Author": "Elena Aledo [aut, cre, cph], Juan-Carlos Aledo [aut]\n(<https://orcid.org/0000-0002-3497-9945>)",
  "Maintainer": "Elena Aledo <elenaaledoesteban@gmail.com>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://ealedo.r-universe.dev",
  "Date/Publication": "2025-04-30 08:50:02 UTC",
  "RemoteUrl": "https://github.com/cran/orthGS",
  "RemoteRef": "HEAD",
  "RemoteSha": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
  "_user": "ealedo",
  "_type": "src",
  "_file": "orthGS_0.1.8.tar.gz",
  "_fileid": "https://r2.ropensci.org/704fc3c6ad14e9d0b2f6fd62861b40804d542b130be328a979dcdb5e0ae270e0",
  "_filesize": 2894681,
  "_sha256": "704fc3c6ad14e9d0b2f6fd62861b40804d542b130be328a979dcdb5e0ae270e0",
  "_expires": "2027-01-22T07:49:01.000Z",
  "_created": "2026-10-14T07:40:48.000Z",
  "_published": "2026-10-14T07:49:03.245Z",
  "_buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 115739150969,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11877437099"
    },
    {
      "job": 115739150915,
      "time": 159,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11877044059"
    },
    {
      "job": 115739150886,
      "time": 247,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11877981902"
    },
    {
      "job": 115739150827,
      "time": 242,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11876984905"
    },
    {
      "job": 115737938738,
      "time": 198,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11878000431"
    },
    {
      "job": 115739150825,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11877616117"
    },
    {
      "job": 115739150862,
      "time": 105,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11876954367"
    },
    {
      "job": 115739150836,
      "time": 110,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11877447891"
    },
    {
      "job": 115739150883,
      "time": 106,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11877149082"
    }
  ],
  "_upstream": "https://github.com/cran/orthGS",
  "_commit": {
    "id": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
    "author": "Elena Aledo <elenaaledoesteban@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.8\n",
    "time": 1746003002
  },
  "_maintainer": {
    "name": "Elena Aledo",
    "email": "elenaaledoesteban@gmail.com",
    "login": "ealedo",
    "description": "I am a graduate student  of Biochemistry ",
    "uuid": 168272167
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "bio3d",
      "role": "Imports"
    },
    {
      "package": "castor",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "TreeTools",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "fs",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "muscle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ealedo",
      "count": 3,
      "uuid": 168272167
    }
  ],
  "_userbio": {
    "uuid": 168272167,
    "type": "user",
    "name": "Elena Aledo",
    "followers": 0,
    "description": "I am a graduate student  of Biochemistry "
  },
  "_downloads": {
    "count": 363,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/orthGS"
  },
  "_searchresults": 56,
  "_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/orthGS.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "ealedo",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.5",
      "date": "2024-09-17"
    },
    {
      "version": "0.1.6",
      "date": "2024-12-02"
    },
    {
      "version": "0.1.8",
      "date": "2025-04-30"
    }
  ],
  "_exports": [
    "coltips",
    "gapless_msa",
    "getseqGS",
    "madRoot",
    "mapTrees",
    "mltree",
    "msa",
    "orthG",
    "orthology",
    "orthP",
    "speciesGS",
    "subsetGS"
  ],
  "_datasets": [
    {
      "name": "A_selected",
      "title": "Adjacency Matrix for Orthology Graph",
      "object": "A_selected",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Sly_GS1b_1",
        "Sly_GS1b_4",
        "Ath_GS1b_1",
        "Ath_GS1b_2",
        "Ath_GS1b_4",
        "Ltu_GS1b_1",
        "Mg_GS1b_1",
        "Vvi_GS1b_2",
        "Vvi_GS1b_1",
        "Ptr_GS1b_3",
        "Ptr_GS1b_4",
        "Ltu_GS1b_2",
        "Lc_GS1b_1",
        "Mg_GS1b_3",
        "Aco_GS1b_1",
        "Aco_GS1b_2",
        "Ptr_GS1b_1",
        "Ptr_GS1b_2",
        "Vvi_GS1b_3",
        "Ltu_GS1b_4",
        "Lc_GS1b_2",
        "Ltu_GS1b_3",
        "Mac_GS1b_6",
        "Ltu_GS1b_5",
        "Lc_GS1b_3",
        "Mg_GS1b_2",
        "Atr_GS1b_1",
        "Ath_GS1b_3",
        "Ath_GS1b_5",
        "Sly_GS1b_3",
        "Mac_GS1b_1",
        "Mac_GS1b_2",
        "Mac_GS1b_3",
        "Osa_GS1b_2",
        "Bdi_GS1b_3",
        "Zm_GS1b_1",
        "Zm_GS1b_5",
        "Mac_GS1b_4",
        "Mac_GS1b_5",
        "Osa_GS1b_3",
        "Bdi_GS1b_2",
        "Zm_GS1b_2",
        "Zm_GS1b_3",
        "Zm_GS1b_4",
        "Osa_GS1b_1",
        "Bdi_GS1b_1",
        "Sly_GS1b_2",
        "Atr_GS1b_2",
        "Gma_GS1b_3",
        "Gma_GS1b_4",
        "Gma_GS1b_1x",
        "Gma_GS1b_1y",
        "Gma_GS1b_2",
        "Gma_GS1b_5",
        "Gma_GS1b_6",
        "Ptr_GS1b_5",
        "Ame_GS1b",
        "Tor_GS1b",
        "Cep_GS1b",
        "Tax_GS1b",
        "Tba_GS1b",
        "Cun_GS1b",
        "Met_GS1b",
        "Pla_GS1b",
        "Fok_GS1b",
        "Pod_GS1b",
        "Nag_GS1b",
        "Sci_GS1b_x",
        "Sci_GS1b_y",
        "Ara_GS1b",
        "Cyc_GS1b",
        "Cha_GS1b",
        "Zam_GS1b",
        "Gin_GS1b_1",
        "Gin_GS1b_2",
        "Gin_GS1b_3",
        "Pp_GS1b_1",
        "Psy_GS1b_1",
        "Pta_GS1b_1",
        "Pin_GS1b_1",
        "Pl_GS1b_1",
        "Pa_GS1b_1",
        "Pg_GS1b_1",
        "Pe_GS1b_1",
        "Psm_GS1b_1",
        "Pta_GS1b_2",
        "Psy_GS1b_2",
        "Pp_GS1b_2",
        "Pl_GS1b_2",
        "Pg_GS1b_2",
        "Pe_GS1b_2",
        "Pa_GS1b_2",
        "Psm_GS1b_2",
        "Pin_GS1b_2",
        "Abi_GS1b_1",
        "Ap_GS1b",
        "Gne_GS1b",
        "Wel_GS1b",
        "Eph_GS1bx",
        "Eph_GS1by",
        "Ltu_GS1a",
        "Lc_GS1a",
        "Mg_GS1a",
        "Atr_GS1a",
        "Met_GS1a",
        "Fok_GS1a",
        "Cun_GS1a",
        "Pla_GS1a",
        "Ame_GS1a",
        "Tor_GS1a",
        "Tax_GS1a",
        "Tba_GS1a",
        "Cep_GS1a",
        "Sci_GS1a",
        "Pod_GS1a",
        "Nag_GS1a",
        "Ara_GS1a",
        "Gin_GS1a",
        "Cyc_GS1a",
        "Cha_GS1a",
        "Zam_GS1a",
        "Eph_GS1a",
        "Gne_GS1a",
        "Wel_GS1a",
        "Psm_GS1a",
        "Pa_GS1a",
        "Pg_GS1a",
        "Pe_GS1a",
        "Abi_GS1a",
        "Ap_GS1a",
        "Pin_GS1a",
        "Pl_GS1a",
        "Pp_GS1a",
        "Psy_GS1a",
        "Pta_GS1a",
        "Vvi_GS2_1",
        "Vvi_GS2_2",
        "Gma_GS2",
        "Ltu_GS2",
        "Lc_GS2",
        "Mg_GS2",
        "Ptr_GS2_1",
        "Ptr_GS2_2",
        "Mac_GS2_1",
        "Mac_GS2_2",
        "Aco_GS2",
        "Osa_GS2",
        "Bdi_GS2_1",
        "Zm_GS2",
        "Sly_GS2",
        "Ath_GS2",
        "Atr_GS2",
        "Cyc_GS2",
        "Cha_GS2",
        "Gin_GS2"
      ],
      "rows": 155,
      "table": true,
      "tojson": true
    },
    {
      "name": "agf",
      "title": "Angiosperms Gymnosperms Ferns",
      "object": "agf",
      "class": [
        "data.frame"
      ],
      "fields": [
        "n",
        "phylo_id",
        "species",
        "taxon",
        "dna",
        "prot",
        "short",
        "gs",
        "pI",
        "factor",
        "size",
        "CSpos",
        "prediction",
        "Lk_SP",
        "Lk_mTP",
        "Lk_cTP",
        "Lk_Thylak",
        "secAa",
        "core",
        "database",
        "acc",
        "up_id",
        "note"
      ],
      "rows": 275,
      "table": true,
      "tojson": true
    },
    {
      "name": "AngGym",
      "title": "Angiosperms Gymnosperms",
      "object": "AngGym",
      "class": [
        "data.frame"
      ],
      "fields": [
        "n",
        "phylo_id",
        "species",
        "taxon",
        "class",
        "dna",
        "prot",
        "short",
        "gsLineage",
        "plant_group"
      ],
      "rows": 155,
      "table": true,
      "tojson": true
    },
    {
      "name": "sdf",
      "title": "Seed Plants and Ferns GS",
      "object": "sdf",
      "class": [
        "data.frame"
      ],
      "fields": [
        "n",
        "Sec.Name_",
        "species",
        "taxon",
        "short",
        "gs",
        "tax_group"
      ],
      "rows": 196,
      "table": true,
      "tojson": true
    },
    {
      "name": "selected_tr",
      "title": "Ultrametric Rooted Seed Plants Tree",
      "object": "selected_tr",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "A_selected",
      "title": "Adjacency Matrix for Orthology Graph",
      "topics": [
        "A_selected"
      ]
    },
    {
      "page": "agf",
      "title": "Angiosperms Gymnosperms Ferns",
      "topics": [
        "agf"
      ]
    },
    {
      "page": "AngGym",
      "title": "Angiosperms Gymnosperms",
      "topics": [
        "AngGym"
      ]
    },
    {
      "page": "coltips",
      "title": "Colouring Tree Tips",
      "topics": [
        "coltips"
      ]
    },
    {
      "page": "gapless_msa",
      "title": "Remove Gaps in a MSA",
      "topics": [
        "gapless_msa"
      ]
    },
    {
      "page": "getseqGS",
      "title": "Get the GS Sequence",
      "topics": [
        "getseqGS"
      ]
    },
    {
      "page": "madRoot",
      "title": "Find The Root of a Phylogenetic Tree Using MAD Method",
      "topics": [
        "madRoot"
      ]
    },
    {
      "page": "mapTrees",
      "title": "Map Gene Tree into Species Tree",
      "topics": [
        "mapTrees"
      ]
    },
    {
      "page": "mltree",
      "title": "Build Up a ML Tree",
      "topics": [
        "mltree"
      ]
    },
    {
      "page": "msa",
      "title": "Multiple Sequence Alignment",
      "topics": [
        "msa"
      ]
    },
    {
      "page": "orthG",
      "title": "Infer GS OrthoGroups Within a Set of Species",
      "topics": [
        "orthG"
      ]
    },
    {
      "page": "orthology",
      "title": "Infer OrthoGroups Using Tree Reconciliation",
      "topics": [
        "orthology"
      ]
    },
    {
      "page": "orthP",
      "title": "Search Orthologous of a Given Protein",
      "topics": [
        "orthP"
      ]
    },
    {
      "page": "sdf",
      "title": "Seed Plants and Ferns GS",
      "topics": [
        "sdf"
      ]
    },
    {
      "page": "selected_tr",
      "title": "Ultrametric Rooted Seed Plants Tree",
      "topics": [
        "selected_tr"
      ]
    },
    {
      "page": "speciesGS",
      "title": "Map Species Names",
      "topics": [
        "speciesGS"
      ]
    },
    {
      "page": "subsetGS",
      "title": "GS Proteins Report",
      "topics": [
        "subsetGS"
      ]
    }
  ],
  "_readme": "https://github.com/cran/orthGS/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "ape",
    "bio3d",
    "bit",
    "bit64",
    "castor",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "cpp11",
    "DEoptim",
    "digest",
    "doParallel",
    "expm",
    "fastmatch",
    "foreach",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "jsonlite",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "naturalsort",
    "nlme",
    "numDeriv",
    "optimParallel",
    "phangorn",
    "phytools",
    "pixmap",
    "pkgconfig",
    "PlotTools",
    "quadprog",
    "rbibutils",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "rlang",
    "RSpectra",
    "scatterplot3d",
    "segmented",
    "seqinr",
    "sp",
    "TreeTools",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "Orthology-Beyond-GS.Rmd",
      "filename": "Orthology-Beyond-GS.html",
      "title": "Orthology Beyond GS",
      "author": "Juan Carlos Aledo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What happen if I am interested in a gene family other than GS?",
        "A toy example"
      ],
      "created": "2025-04-30 08:50:02",
      "modified": "2025-04-30 08:50:02",
      "commits": 1
    },
    {
      "source": "Performing-Sequence-Alignment-in-R.Rmd",
      "filename": "Performing-Sequence-Alignment-in-R.html",
      "title": "Performing Sequence Alignment in R",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Downloading and installing MUSCLE and Clustal Omega",
        "Performing alignment using the orthGS package",
        "Performing alignment using the ape package",
        "Performing alignment using the msa package",
        "Performing alignment using the muscle package",
        "Performing alignment integrating MUSCLE v5 in your R workflow"
      ],
      "created": "2025-04-30 08:50:02",
      "modified": "2025-04-30 08:50:02",
      "commits": 1
    },
    {
      "source": "Searching-for-Orthologous.Rmd",
      "filename": "Searching-for-Orthologous.html",
      "title": "Searching for GS Orthologs",
      "author": "Elena Aledo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Orthologs from crop in model plants and vice versa"
      ],
      "created": "2025-04-30 08:50:02",
      "modified": "2025-04-30 08:50:02",
      "commits": 1
    },
    {
      "source": "Unraveling-the-Hiden-Paralogs.Rmd",
      "filename": "Unraveling-the-Hiden-Paralogs.html",
      "title": "Unraveling the Hiden Paralogs",
      "author": "Elena Aledo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Orthologs versus paralogs",
        "Glutamine synthetase from conifers",
        "Phylogenetic reconciliation",
        "GS1a orthology network beyond conifers",
        "References"
      ],
      "created": "2025-04-30 08:50:02",
      "modified": "2025-04-30 08:50:02",
      "commits": 1
    }
  ],
  "_score": 4.049218022670182,
  "_indexed": true,
  "_nocasepkg": "orthgs",
  "_universes": [
    "ealedo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.8",
      "date": "2026-10-14T07:42:52.000Z",
      "distro": "resolute",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/bab3d0efacf10d7cf5996a05a56afefd93efe054c71e680a57a930cc7428de2e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.8",
      "date": "2026-10-14T07:43:05.000Z",
      "distro": "resolute",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/52361df4fb99b7441cbd944ce341413ec842821dd4e51778403d4764e81b35b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.8",
      "date": "2026-10-14T07:47:04.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/7248b3072f9c674f924db6f3e92c0554f954308ccb1bbb8f27cc986382dd18a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.8",
      "date": "2026-10-14T07:46:16.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/6220021c5d3b08d824c8f62a20d828c15669046f4a9925bd19b5dbe284469972",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.8",
      "date": "2026-10-14T07:43:13.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/5890964b419a240cb24247b911893a9aeb1af3e5a5d35ea8450255b7d5863865",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-14T07:42:01.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/0b6dd974a395c76989fd809934ac83b14ac6229d2a0f361e92eead42f9899fb5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-14T07:42:10.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/578df839cce39f9d344afb0f51234b9d19f3abe2e9eb549de31fa624df3cebee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-14T07:42:07.000Z",
      "commit": "df5ff31aa538fabda5b8cfc046f66b1471d8cdc8",
      "fileid": "https://r2.ropensci.org/7ec5fcdf24afa471db2c54fcecfd98d182aa556a5e5211f55646cd23d0f97976",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ealedo/actions/runs/38529538132"
    }
  ]
}