{ "_id": "6ad00559e2d863f662953b33", "Package": "linkmapper", "Title": "Point-and-Click Linkage Mapping and QTL Analysis", "Version": "0.2.0", "Authors@R": "c(\nperson(\"Ebenezer\", \"Ogoe\", , \"ebenezerogoe@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = \"Co-creator; wrote the 2026 package\"),\nperson(\"Michael\", \"Obeng\", role = c(\"aut\", \"cph\"),\ncomment = \"Co-creator of Linkmapper (2022)\"),\nperson(\"Stephen\", \"Amoako\", role = c(\"aut\", \"cph\"),\ncomment = \"Co-creator of Linkmapper (2022)\")\n)", "Description": "A 'shiny' application and a set of plain R functions for\nbuilding genetic linkage maps and locating quantitative trait\nloci in F2 intercross, backcross and recombinant inbred line\npopulations. It wraps 'onemap' (Margarido et al. 2007\n) for segregation tests,\ntwo-point analysis, grouping, ordering and map estimation, and\n'qtl' (Broman et al. 2003 )\nfor interval mapping and composite interval mapping with\npermutation thresholds. Results can be exported as figures,\ntables, a self-contained HTML report and an R script that\nreproduces the analysis.", "License": "MIT + file LICENSE", "URL": "https://github.com/ebenogoe/linkmapper,\nhttps://ebenogoe.github.io/linkmapper/", "BugReports": "https://github.com/ebenogoe/linkmapper/issues", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev make libharfbuzz-dev libicu-dev\nlibpng-dev libuv1-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://ebenogoe.r-universe.dev", "Date/Publication": "2026-10-14 19:33:53 UTC", "RemoteUrl": "https://github.com/ebenogoe/linkmapper", "RemoteRef": "main", "RemoteSha": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-14 22:33:31 UTC", "User": "root" }, "Author": "Ebenezer Ogoe [aut, cre, cph] (Co-creator; wrote the 2026 package),\nMichael Obeng [aut, cph] (Co-creator of Linkmapper (2022)),\nStephen Amoako [aut, cph] (Co-creator of Linkmapper (2022))", "Maintainer": "Ebenezer Ogoe ", "_user": "ebenogoe", "_type": "src", "_file": "linkmapper_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/9686814f9134fe10e3a1619a8b5fe180d191857b886dc079c9ed2a38955daf83", "_filesize": 1510414, "_sha256": "9686814f9134fe10e3a1619a8b5fe180d191857b886dc079c9ed2a38955daf83", "_expires": "2027-01-22T22:42:31.000Z", "_created": "2026-10-14T22:33:31.000Z", "_published": "2026-10-14T22:42:33.682Z", "_buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116141238062, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11934015678" }, { "job": 116141238121, "time": 188, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11933402584" }, { "job": 116141238204, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11933547536" }, { "job": 116141238069, "time": 122, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11933926502" }, { "job": 116139671100, "time": 244, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11933940095" }, { "job": 116141238154, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11933417477" }, { "job": 116141238163, "time": 117, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11933223911" }, { "job": 116141238223, "time": 125, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11933930619" }, { "job": 116141238201, "time": 117, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11933815591" } ], "_upstream": "https://github.com/ebenogoe/linkmapper", "_commit": { "id": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "author": "Ebenezer Ogoe ", "committer": "Ebenezer Ogoe ", "message": "Fix guided tour; full-height page layout without sideways scroll\n", "time": 1792006433 }, "_maintainer": { "name": "Ebenezer Ogoe", "email": "ebenezerogoe@gmail.com", "login": "ebenogoe", "linkedin": "in/ebenogoe", "description": "", "uuid": 12881069 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "bsicons", "role": "Imports" }, { "package": "bslib", "version": ">= 0.8.0", "role": "Imports" }, { "package": "cicerone", "role": "Imports" }, { "package": "config", "role": "Imports" }, { "package": "ggiraph", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "golem", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "onemap", "role": "Imports" }, { "package": "qtl", "role": "Imports" }, { "package": "reactable", "role": "Imports" }, { "package": "shiny", "version": ">= 1.8.1", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "svglite", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "writexl", "role": "Imports" }, { "package": "chromote", "role": "Suggests" }, { "package": "pkgload", "role": "Suggests" }, { "package": "shinytest2", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ebenogoe", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-26", "n": 5 }, { "week": "2026-42", "n": 2 } ], "_tags": [], "_topics": [ "gene-map", "linkage-mapping", "open-source", "qtl-mapping", "r-shiny" ], "_stars": 0, "_contributors": [ { "user": "ebenogoe", "count": 7, "uuid": 12881069 } ], "_userbio": { "uuid": 12881069, "type": "user", "name": "Ebenezer Ogoe", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/linkmapper" }, "_devurl": "https://github.com/ebenogoe/linkmapper", "_pkgdown": "https://ebenogoe.github.io/linkmapper/", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/linkmapper.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "add_traits", "build_cross", "build_report", "build_script", "default_settings", "demo_info", "filter_markers", "genotype_effect", "group_markers", "linkage_groups", "linkmapper_demo", "load_session", "map_plot_size", "map_positions", "map_summary", "order_groups", "order_methods", "plot_effect", "plot_linkage_map", "plot_lod", "plot_missing", "plot_rf_heatmap", "plot_segregation", "qc_summary", "qtl_methods", "read_cross", "run_analysis", "run_app", "run_linkmapper", "save_session", "scan_qtl", "suggest_lod", "theme_linkmapper", "validate_lm_file", "write_mapmaker" ], "_help": [ { "page": "add_traits", "title": "Add trait values to a dataset", "topics": [ "add_traits" ] }, { "page": "build_cross", "title": "Build an R/qtl cross from a Linkmapper map", "topics": [ "build_cross" ] }, { "page": "build_report", "title": "Write a self-contained HTML report", "topics": [ "build_report" ] }, { "page": "build_script", "title": "Write an R script that repeats an analysis", "topics": [ "build_script" ] }, { "page": "default_settings", "title": "Default analysis settings", "topics": [ "default_settings" ] }, { "page": "demo_info", "title": "Demo datasets", "topics": [ "demo_info", "linkmapper_demo" ] }, { "page": "filter_markers", "title": "Filter markers", "topics": [ "filter_markers" ] }, { "page": "genotype_effect", "title": "Trait values by genotype at a marker", "topics": [ "genotype_effect" ] }, { "page": "group_markers", "title": "Group markers (Linkmapper 0.1 interface)", "topics": [ "group_markers" ] }, { "page": "linkage_groups", "title": "Find linkage groups", "topics": [ "linkage_groups" ] }, { "page": "map_plot_size", "title": "Size of a linkage map figure in inches", "topics": [ "map_plot_size" ] }, { "page": "map_positions", "title": "Marker positions on a map", "topics": [ "map_positions" ] }, { "page": "map_summary", "title": "Summary of each linkage group", "topics": [ "map_summary" ] }, { "page": "order_groups", "title": "Order markers within each linkage group", "topics": [ "order_groups" ] }, { "page": "order_methods", "title": "Ordering algorithms", "topics": [ "order_methods" ] }, { "page": "plot_effect", "title": "Trait values by genotype", "topics": [ "plot_effect" ] }, { "page": "plot_linkage_map", "title": "Draw a linkage map", "topics": [ "plot_linkage_map" ] }, { "page": "plot_lod", "title": "LOD profile plot", "topics": [ "plot_lod" ] }, { "page": "plot_missing", "title": "Missing data plot", "topics": [ "plot_missing" ] }, { "page": "plot_rf_heatmap", "title": "Recombination fraction heatmap for one linkage group", "topics": [ "plot_rf_heatmap" ] }, { "page": "plot_segregation", "title": "Segregation test plot", "topics": [ "plot_segregation" ] }, { "page": "qc_summary", "title": "Marker and individual quality summary", "topics": [ "qc_summary" ] }, { "page": "qtl_methods", "title": "QTL mapping methods", "topics": [ "qtl_methods" ] }, { "page": "read_cross", "title": "Read a genotype file", "topics": [ "read_cross" ] }, { "page": "run_analysis", "title": "Run a whole analysis from settings", "topics": [ "run_analysis" ] }, { "page": "run_app", "title": "Run the Linkmapper app", "topics": [ "run_app", "run_linkmapper" ] }, { "page": "save_session", "title": "Save and restore an analysis session", "topics": [ "load_session", "save_session" ] }, { "page": "scan_qtl", "title": "Scan for QTL", "topics": [ "scan_qtl" ] }, { "page": "suggest_lod", "title": "Suggest a LOD threshold", "topics": [ "suggest_lod" ] }, { "page": "theme_linkmapper", "title": "ggplot2 theme used by Linkmapper", "topics": [ "theme_linkmapper" ] }, { "page": "validate_lm_file", "title": "Check that a file can be read", "topics": [ "validate_lm_file" ] }, { "page": "write_mapmaker", "title": "Write a dataset in MAPMAKER format", "topics": [ "write_mapmaker" ] } ], "_readme": "https://github.com/ebenogoe/linkmapper/raw/main/README.md", "_rundeps": [ "abind", "ape", "askpass", "assertthat", "attempt", "backports", "base64enc", "bit", "bit64", "boot", "broom", "bsicons", "bslib", "cachem", "car", "carData", "checkmate", "cicerone", "class", "cli", "clipr", "cluster", "codetools", "colorspace", "commonmark", "config", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "dendextend", "Deriv", "digest", "doBy", "doParallel", "dplyr", "e1071", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "foreach", "forecast", "foreign", "Formula", "fracdiff", "fs", "gdata", "gdtools", "generics", "ggiraph", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glmnet", "glue", "golem", "gridExtra", "gtable", "gtools", "haven", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "isoband", "iterators", "jomo", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "memuse", "mgcv", "mice", "mime", "minqa", "mitml", "modelr", "nlme", "nloptr", "nnet", "nnls", "numDeriv", "onemap", "openssl", "ordinal", "otel", "pan", "pbkrtest", "permute", "pillar", "pinfsc50", "pkgconfig", "plotly", "plotrix", "plyr", "polynom", "prettyunits", "princurve", "progress", "promises", "proxy", "purrr", "qtl", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reactable", "reactR", "readr", "reformulas", "reshape2", "rlang", "rmarkdown", "rpart", "rstatix", "rstudioapi", "S7", "sass", "scales", "shape", "shiny", "smacof", "sourcetools", "SparseM", "stringi", "stringr", "survival", "svglite", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "tzdb", "ucminf", "urca", "utf8", "vcfR", "vctrs", "vegan", "viridis", "viridisLite", "vroom", "weights", "withr", "wordcloud", "writexl", "xfun", "xtable", "yaml", "zoo" ], "_score": 2, "_indexed": true, "_nocasepkg": "linkmapper", "_universes": [ "ebenogoe" ], "_previous": "0.1.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-10-14T22:36:25.000Z", "distro": "resolute", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/c86649e0e44bdd10f6954dd51a9b0d8bcf5e9e49b62400d9e7b4c2ad35899efb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-10-14T22:36:25.000Z", "distro": "resolute", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/060467938268ebc19c12cdab494cedbcb6744ded45f5ca88a11e2537a8fec81b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-10-14T22:41:38.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/ed2ed65c3e9b8ee92e89d25684919e046548a18b2c95174de755fea00f96d789", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.6.1", "os": "mac", "version": "0.2.0", "date": "2026-10-14T22:40:25.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/dfcecab1a08ccf43255ab258f39c12f02e3efb39ef922c14444614983e84ffa7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-10-14T22:36:26.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/3f75133fc3451613af9bfd17f15839074a46288d0153b5f66eac0cfff0ef32e3", "status": "success", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-10-14T22:35:02.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/107146596a9e6d41d988a7e6666c8b52f6b7a72a1f6ad8ee7d863158aff299e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-10-14T22:35:09.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/46e314602676805f99339cd6266e05b83ca78178d2bca50011c010617253a7f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" }, { "r": "4.6.1", "os": "win", "version": "0.2.0", "date": "2026-10-14T22:35:01.000Z", "commit": "a75c2a9a05f7323fad8ba3fbeff2074c72554092", "fileid": "https://r2.ropensci.org/4ea2561d3ed5ff1e83ecccdc53c53fb43661bb1fa9118f25a4a6ebedee4a7a96", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ebenogoe/actions/runs/38647998162" } ] }