{ "_id": "6a509d6389c83ec243a2ea02", "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": "2026-07-10 07:13:07 UTC", "User": "root" }, "Author": "Kristian K Ullrich [aut, cre] (ORCID:\n)", "Maintainer": "Kristian K Ullrich ", "_user": "kullrich", "_type": "src", "_file": "CRBHits_0.0.10.tar.gz", "_fileid": "https://r2.ropensci.org/73c8382e0f1aa85d82497e378df107d56343c435bf8cd6dd864ea4c585d900c1", "_filesize": 20553939, "_sha256": "73c8382e0f1aa85d82497e378df107d56343c435bf8cd6dd864ea4c585d900c1", "_expires": "2026-10-18T07:21:04.000Z", "_created": "2026-07-10T07:13:07.000Z", "_published": "2026-07-10T07:21:07.598Z", "_jobs": [ { "job": 86307765984, "time": 350, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8220858163" }, { "job": 86307765987, "time": 408, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8220877657" }, { "job": 86307766001, "time": 348, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8220843461" }, { "job": 86307766036, "time": 394, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8220862101" }, { "job": 86306843914, "time": 357, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8220737819" }, { "job": 86307766022, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8220794468" }, { "job": 86307766024, "time": 229, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8220817799" }, { "job": 86307766021, "time": 240, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8220821544" }, { "job": 86307766000, "time": 236, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8220820731" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790", "_status": "success", "_upstream": "https://github.com/kullrich/crbhits", "_commit": { "id": "158ea52a96bbcb0928e384ac15015597aaa987bc", "author": "Kristian Ullrich ", "committer": "Kristian Ullrich ", "message": "# work on external tools\n", "time": 1747846441 }, "_maintainer": { "name": "Kristian K Ullrich", "email": "ullrich@evolbio.mpg.de", "login": "kullrich", "orcid": "0000-0003-4308-9626", "description": "", "uuid": 8100643 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "MSA2dist", "version": ">= 1.12.0", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "seqinr", "role": "Suggests" }, { "package": "stringi", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" } ], "_owner": "kullrich", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "software", "alignment", "genetics", "bioinformatics", "dnds", "dnds-estimation", "joss", "kaks", "last", "pairwise-comparison", "reciprocal-blast-hits", "synteny" ], "_stars": 4, "_contributors": [ { "user": "kullrich", "count": 312, "uuid": 8100643 } ], "_userbio": { "uuid": 8100643, "type": "user", "name": "Kristian Ullrich", "followers": 35 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CRBHits" }, "_devurl": "https://github.com/kullrich/crbhits", "_pkgdown": "https://kullrich.github.io/CRBHits/", "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CRBHits.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "aa2rbh", "aadir2orthofinder", "aafile2rbh", "aafile2rbhplus", "cds2genepos", "cds2rbh", "cdsdir2orthofinder", "cdsfile2aafile", "cdsfile2rbh", "check_ext_install", "col2transparent", "CRBHitsColors", "filter_alnlen", "filter_eval", "filter_pident", "filter_qcov", "filter_rost1999", "filter_tcov", "gff2longest", "gtf2longest", "isoform2longest", "make_dagchainer", "make_last", "make_vignette", "plot_dagchainer", "plot_kaks", "rbh2dagchainer", "rbh2kaks", "seqid", "tandemdups" ], "_datasets": [ { "name": "aly", "title": "aly-data", "object": "aly", "file": "aly.rda", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false }, { "name": "ath", "title": "ath-data", "object": "ath", "file": "ath.rda", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false }, { "name": "ath_aly_crbh", "title": "ath_aly_crbh-data", "object": "ath_aly_crbh", "file": "ath_aly_crbh.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ath_aly_ncbi_dagchainer", "title": "ath_aly_ncbi_dagchainer-data", "object": "ath_aly_ncbi_dagchainer", "file": "ath_aly_ncbi_dagchainer.rda", "class": [ "data.frame" ], "fields": [ "gene1.chr", "gene1.seq.id", "gene1.start", "gene1.end", "gene1.mid", "gene1.idx", "gene2.chr", "gene2.seq.id", "gene2.start", "gene2.end", "gene2.mid", "gene2.idx", "evalue", "score", "dagchainer_group" ], "rows": 25007, "table": true, "tojson": true }, { "name": "ath_aly_ncbi_kaks", "title": "ath_aly_ncbi_kaks-data", "object": "ath_aly_ncbi_kaks", "file": "ath_aly_ncbi_kaks.rda", "class": [ "data.frame" ], "fields": [ "aa1", "aa2", "rbh_class", "ka", "ks", "vka", "vks" ], "rows": 32192, "table": true, "tojson": true }, { "name": "hom_pan_ensembl_kaks", "title": "hom_pan_ensembl_kaks-data", "object": "hom_pan_ensembl_kaks", "file": "hom_pan_ensembl_kaks.rda", "class": [ "data.frame" ], "fields": [ "aa1", "aa2", "rbh_class", "ka", "ks", "vka", "vks" ], "rows": 24602, "table": true, "tojson": true } ], "_help": [ { "page": "aa2rbh", "title": "aa2rbh", "topics": [ "aa2rbh" ] }, { "page": "aadir2orthofinder", "title": "aadir2orthofinder", "topics": [ "aadir2orthofinder" ] }, { "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": [ "ath_aly_ncbi_dagchainer", "ath_aly_ncbi_dagchainer-data" ] }, { "page": "ath_aly_ncbi_kaks-data", "title": "ath_aly_ncbi_kaks-data", "topics": [ "ath_aly_ncbi_kaks", "ath_aly_ncbi_kaks-data" ] }, { "page": "ath-data", "title": "ath-data", "topics": [ "ath", "ath-data" ] }, { "page": "cds2genepos", "title": "cds2genepos", "topics": [ "cds2genepos" ] }, { "page": "cds2rbh", "title": "cds2rbh", "topics": [ "cds2rbh" ] }, { "page": "cdsdir2orthofinder", "title": "cdsdir2orthofinder", "topics": [ "cdsdir2orthofinder" ] }, { "page": "cdsfile2aafile", "title": "cdsfile2aafile", "topics": [ "cdsfile2aafile" ] }, { "page": "cdsfile2rbh", "title": "cdsfile2rbh", "topics": [ "cdsfile2rbh" ] }, { "page": "check_ext_install", "title": "check_ext_install", "topics": [ "check_ext_install" ] }, { "page": "col2transparent", "title": "col2transparent", "topics": [ "col2transparent" ] }, { "page": "CRBHitsColors", "title": "CRBHitsColors", "topics": [ "CRBHitsColors" ] }, { "page": "filter_alnlen", "title": "filter_alnlen", "topics": [ "filter_alnlen" ] }, { "page": "filter_eval", "title": "filter_eval", "topics": [ "filter_eval" ] }, { "page": "filter_pident", "title": "filter_pident", "topics": [ "filter_pident" ] }, { "page": "filter_qcov", "title": "filter_qcov", "topics": [ "filter_qcov" ] }, { "page": "filter_rost1999", "title": "filter_rost1999", "topics": [ "filter_rost1999" ] }, { "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": [ "ade4", "ape", "BiocGenerics", "Biostrings", "bit", "bit64", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "digest", "doParallel", "dplyr", "farver", "foreach", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "hms", "IRanges", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "MSA2dist", "MultipleAlignment", "nlme", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "purrr", "pwalign", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppThread", "readr", "rlang", "S4Vectors", "S7", "scales", "segmented", "Seqinfo", "seqinr", "sp", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "XVector" ], "_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 } ], "_score": 3.6812412373755876, "_indexed": true, "_nocasepkg": "crbhits", "_universes": [ "kullrich" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.10", "date": "2026-07-10T07:16:15.000Z", "distro": "resolute", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/db5cc95912d00a941a39f6e678c71ef84799027fd4cc634266107bdef5b41d74", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.6.1", "os": "linux", "version": "0.0.10", "date": "2026-07-10T07:16:15.000Z", "distro": "resolute", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/428b2913f8e30fbe01ab00d418bacd334e13b1f4ae99a29e516f9c907e472a8f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.5.3", "os": "mac", "version": "0.0.10", "date": "2026-07-10T07:15:39.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/c80cc05b10457b61f8b45ae0a849177772ed7beffeec2d27b6401dcc1991d1e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.6.1", "os": "mac", "version": "0.0.10", "date": "2026-07-10T07:16:14.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/362dcad2dc32197ff977908e66b838390e401e0f5d6905b342066f141c68750f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.10", "date": "2026-07-10T07:16:21.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/197b1aa6bc5ecf2e0cb052205b9a7c96f9c2127d4d83208f872446c1eb68c43a", "status": "success", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.7.0", "os": "win", "version": "0.0.10", "date": "2026-07-10T07:14:56.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/0669ed5f01b87d2079a402601a6b2caaf17bb84c385f007b9a83d6254b9c5146", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.5.3", "os": "win", "version": "0.0.10", "date": "2026-07-10T07:15:12.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/0af8f977bab3f2bb74d7dc5cc3f9a70ee9ca7da5a856404df0d2577db473c2b1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" }, { "r": "4.6.1", "os": "win", "version": "0.0.10", "date": "2026-07-10T07:15:11.000Z", "commit": "158ea52a96bbcb0928e384ac15015597aaa987bc", "fileid": "https://r2.ropensci.org/47a7088c21c3ec44b0981b4392563b71a562be60efd8244c4c0f1781d27e98ab", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/kullrich/actions/runs/29075737790" } ] }