{
  "_id": "6a103ddfacfb0bcc41c9c641",
  "Package": "CRBHits",
  "Title": "Conditional reciprocal best hits (CRBHits) in R",
  "Version": "0.0.10",
  "Authors@R": "person(given = \"Kristian K\",\nfamily = \"Ullrich\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ullrich@evolbio.mpg.de\",\ncomment = c(ORCID = \"0000-0003-4308-9626\"))",
  "Description": "CRBHits calculates conditional reciprocal best hit\n(CRBHit) pairs and subsequently can classify tandem duplicates,\nassign syntney groups and calculate Ka/Ks values.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Alignment, Genetics",
  "NeedsCompilation": "yes",
  "SystemRequirements": "LAST (https://anaconda.org/bioconda/last),\nDAGchainer (https://anaconda.org/bioconda/dagchainer), DIAMOND\n(optional, https://anaconda.org/bioconda/diamond), MMSEQS2\n(optiona, https://anaconda.org/bioconda/mmseqs2), LAMBDA\n(optional, https://anaconda.org/bioconda/lambda), GNU make,\nlibcurl (deb: libcurl4-openssl-dev or CentOS: libcurl-devel),\nopenssl (deb: libssl-dev or CentOS: openssl-devel), libxml2\n(deb: libxml2-dev or CentOS: libxml2-devel), libGLU (deb:\nlibglu1-mesa-dev or CentOS: mesa-libGLU-devel), libgit2-devel\n(deb: libgit2-dev or CentOS: libgit2-devel)",
  "URL": "https://github.com/kullrich/CRBHits,\nhttps://kullrich.github.io/CRBHits/",
  "BugReports": "https://github.com/kullrich/CRBHits/issues",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "make libgit2-dev libicu-dev libxml2-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://kullrich.r-universe.dev",
  "Date/Publication": "2025-05-21 16:54:01 UTC",
  "RemoteUrl": "https://github.com/kullrich/crbhits",
  "RemoteRef": "HEAD",
  "RemoteSha": "158ea52a96bbcb0928e384ac15015597aaa987bc",
  "Packaged": {
    "Date": "2026-05-11 09:31:42 UTC",
    "User": "root"
  },
  "Author": "Kristian K Ullrich [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4308-9626>)",
  "Maintainer": "Kristian K Ullrich <ullrich@evolbio.mpg.de>",
  "MD5sum": "46887db5905d511be0d9bc60d3c03c53",
  "_user": "kullrich",
  "_type": "src",
  "_file": "CRBHits_0.0.10.tar.gz",
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  "_filesize": 20553938,
  "_sha256": "419d1d7ee27e483f60fd5084b8aed046127774f134284a11847b6ba3c2768dfa",
  "_created": "2026-05-11T09:31:42.000Z",
  "_published": "2026-05-22T11:28:31.017Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/kullrich/actions/runs/25661787154",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/kullrich/crbhits",
  "_commit": {
    "id": "158ea52a96bbcb0928e384ac15015597aaa987bc",
    "author": "Kristian Ullrich <ullrich@evolbio.mpg.de>",
    "committer": "Kristian Ullrich <ullrich@evolbio.mpg.de>",
    "message": "# work on external tools\n",
    "time": 1747846441
  },
  "_maintainer": {
    "name": "Kristian K Ullrich",
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      "week": "2025-20",
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  "_tags": [],
  "_topics": [
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    "alignment",
    "genetics",
    "bioinformatics",
    "dnds",
    "dnds-estimation",
    "joss",
    "kaks",
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  "_exports": [
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    "gtf2longest",
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    "make_dagchainer",
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    "make_vignette",
    "plot_dagchainer",
    "plot_kaks",
    "rbh2dagchainer",
    "rbh2kaks",
    "seqid",
    "tandemdups"
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  "_datasets": [
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      "title": "aly-data",
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      "class": [
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      "class": [
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      "table": false,
      "tojson": false
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      "rows": 25007,
      "table": true,
      "tojson": true
    },
    {
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      "title": "ath_aly_ncbi_kaks-data",
      "object": "ath_aly_ncbi_kaks",
      "file": "ath_aly_ncbi_kaks.rda",
      "class": [
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      ],
      "fields": [
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        "aa2",
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        "ks",
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        "vks"
      ],
      "rows": 32192,
      "table": true,
      "tojson": true
    },
    {
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      "object": "hom_pan_ensembl_kaks",
      "file": "hom_pan_ensembl_kaks.rda",
      "class": [
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      "fields": [
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        "ks",
        "vka",
        "vks"
      ],
      "rows": 24602,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aa2rbh",
      "title": "aa2rbh",
      "topics": [
        "aa2rbh"
      ]
    },
    {
      "page": "aadir2orthofinder",
      "title": "aadir2orthofinder",
      "topics": [
        "aadir2orthofinder"
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    },
    {
      "page": "aafile2rbh",
      "title": "aafile2rbh",
      "topics": [
        "aafile2rbh"
      ]
    },
    {
      "page": "aafile2rbhplus",
      "title": "aafile2rbhplus",
      "topics": [
        "aafile2rbhplus"
      ]
    },
    {
      "page": "aly-data",
      "title": "aly-data",
      "topics": [
        "aly",
        "aly-data"
      ]
    },
    {
      "page": "ath_aly_crbh-data",
      "title": "ath_aly_crbh-data",
      "topics": [
        "ath_aly_crbh",
        "ath_aly_crbh-data"
      ]
    },
    {
      "page": "ath_aly_ncbi_dagchainer-data",
      "title": "ath_aly_ncbi_dagchainer-data",
      "topics": [
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        "ath_aly_ncbi_dagchainer-data"
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    {
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      "title": "ath_aly_ncbi_kaks-data",
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        "ath_aly_ncbi_kaks-data"
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    {
      "page": "ath-data",
      "title": "ath-data",
      "topics": [
        "ath",
        "ath-data"
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    },
    {
      "page": "cds2genepos",
      "title": "cds2genepos",
      "topics": [
        "cds2genepos"
      ]
    },
    {
      "page": "cds2rbh",
      "title": "cds2rbh",
      "topics": [
        "cds2rbh"
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    },
    {
      "page": "cdsdir2orthofinder",
      "title": "cdsdir2orthofinder",
      "topics": [
        "cdsdir2orthofinder"
      ]
    },
    {
      "page": "cdsfile2aafile",
      "title": "cdsfile2aafile",
      "topics": [
        "cdsfile2aafile"
      ]
    },
    {
      "page": "cdsfile2rbh",
      "title": "cdsfile2rbh",
      "topics": [
        "cdsfile2rbh"
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    },
    {
      "page": "check_ext_install",
      "title": "check_ext_install",
      "topics": [
        "check_ext_install"
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    },
    {
      "page": "col2transparent",
      "title": "col2transparent",
      "topics": [
        "col2transparent"
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    },
    {
      "page": "CRBHitsColors",
      "title": "CRBHitsColors",
      "topics": [
        "CRBHitsColors"
      ]
    },
    {
      "page": "filter_alnlen",
      "title": "filter_alnlen",
      "topics": [
        "filter_alnlen"
      ]
    },
    {
      "page": "filter_eval",
      "title": "filter_eval",
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    },
    {
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      "title": "filter_pident",
      "topics": [
        "filter_pident"
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    {
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      "topics": [
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      "title": "filter_rost1999",
      "topics": [
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      ]
    },
    {
      "page": "filter_tcov",
      "title": "filter_tcov",
      "topics": [
        "filter_tcov"
      ]
    },
    {
      "page": "gff2longest",
      "title": "gff2longest",
      "topics": [
        "gff2longest"
      ]
    },
    {
      "page": "gtf2longest",
      "title": "gtf2longest",
      "topics": [
        "gtf2longest"
      ]
    },
    {
      "page": "hom_pan_ensembl_kaks-data",
      "title": "hom_pan_ensembl_kaks-data",
      "topics": [
        "hom_pan_ensembl_kaks",
        "hom_pan_ensembl_kaks-data"
      ]
    },
    {
      "page": "isoform2longest",
      "title": "isoform2longest",
      "topics": [
        "isoform2longest"
      ]
    },
    {
      "page": "make_dagchainer",
      "title": "make_dagchainer",
      "topics": [
        "make_dagchainer"
      ]
    },
    {
      "page": "make_last",
      "title": "make_last",
      "topics": [
        "make_last"
      ]
    },
    {
      "page": "make_vignette",
      "title": "make_vignette",
      "topics": [
        "make_vignette"
      ]
    },
    {
      "page": "plot_dagchainer",
      "title": "plot_dagchainer",
      "topics": [
        "plot_dagchainer"
      ]
    },
    {
      "page": "plot_kaks",
      "title": "plot_kaks",
      "topics": [
        "plot_kaks"
      ]
    },
    {
      "page": "rbh2dagchainer",
      "title": "rbh2dagchainer",
      "topics": [
        "rbh2dagchainer"
      ]
    },
    {
      "page": "rbh2kaks",
      "title": "rbh2kaks",
      "topics": [
        "rbh2kaks"
      ]
    },
    {
      "page": "seqid",
      "title": "seqid",
      "topics": [
        "seqid"
      ]
    },
    {
      "page": "tandemdups",
      "title": "tandemdups",
      "topics": [
        "tandemdups"
      ]
    }
  ],
  "_pkglogo": "https://github.com/kullrich/crbhits/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/kullrich/crbhits/raw/HEAD/README.md",
  "_rundeps": [
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  "_vignettes": [
    {
      "source": "V01CRBHitsBasicVignette.Rmd",
      "filename": "V01CRBHitsBasicVignette.html",
      "title": "CRBHits Basic Vignette",
      "author": "Kristian K Ullrich",
      "engine": "knitr::rmarkdown",
      "headings": [
        "CRBHit Basic Vignette",
        "Table of Contents",
        "1. [Installation]",
        "2. [Conditional Reciprocal Best Hits - Algorithm]",
        "2.1. [1. step: sequence similarity search (last)]",
        "2.1.1. [Input: Coding Sequences (CDS)]",
        "2.1.2. [Get Longest Isoform from NCBI or ENSEMBL Input (optional)]",
        "2.1.3. [Sequence Similarity Search]",
        "2.2. [2. step: filter hits + RBH extraction]",
        "2.2.1. [Filter blast-like output prior fitting]",
        "2.2.2. [Custom Filter]",
        "2.2.3. [Extract RBHs]",
        "2.3. [3. step: fitting RBHs + get CRBHs]",
        "2.3.1. [CRBHit pairs - Fitting Parameter]",
        "3. [Ka/Ks Calculations]",
        "3.1. [Codon Alignments - cds2codonaln() Function]",
        "3.2. [MSA2dist::dnastring2kaks() Function]",
        "3.3. [rbh2kaks() Function]",
        "4. [References]"
      ],
      "created": "2020-05-26 14:38:54",
      "modified": "2025-05-16 11:53:11",
      "commits": 31
    },
    {
      "source": "V02KaKsVignette.Rmd",
      "filename": "V02KaKsVignette.html",
      "title": "KaKs Vignette",
      "author": "Kristian K Ullrich",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Ka/Ks Vignette",
        "Table of Contents",
        "1. [Conditional reciprocal best hit pairs]",
        "1.1. [Download Coding sequences (CDS) from NCBI and ENSEMBL]",
        "1.2. [Get Longest Isoform from NCBI or ENSEMBL Input]",
        "1.2.1 [isoform2longest()]",
        "1.2.2 [gtf2longest()]",
        "1.2.3 [gff2longest()]",
        "1.3. [Calculate/Filter CRBHit pairs]",
        "1.4. [Extract Gene/Isoform chromosomal position]",
        "1.4.1. [Get gene position from NCBI or ENSEMBL Input]",
        "1.4.2. [Use GTF/GFF3 file to obtain gene position]",
        "1.5 [Assign Tandem Duplicates]",
        "1.6 [Synteny with DAGchainer]",
        "2. [Ka/Ks Calculation]",
        "3. [Ka/Ks Filtering and Visualisation]",
        "4. [Homo sapiens vs. Pan troglodytes example]",
        "5. [References]"
      ],
      "created": "2020-10-28 18:48:20",
      "modified": "2025-05-16 11:53:11",
      "commits": 31
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