{ "_id": "6a1572c0acfb0bcc41d654fa", "Package": "bexy", "Type": "Package", "Title": "Visualize and Parse the Output of 'BeXY'", "Version": "0.1.3", "Authors@R": "c(person(\"Madleina\", \"Caduff\", \nrole = c(\"aut\", \"cre\"),\nemail = \"madleina.caduff@unifr.ch\"),\nperson(\"Raphael\", \"Eckel\",\nrole = \"ctb\"),\nperson(\"Christoph\", \"Leuenberger\",\nrole = \"ctb\"),\nperson(\"Daniel\", \"Wegmann\",\nrole = \"aut\",\nemail = \"daniel.wegmann@unifr.ch\")\n)", "Maintainer": "Madleina Caduff ", "Description": "Provides functions for summarizing and plotting the output\nof the command-line tool 'BeXY'\n(), a tool that performs\nBayesian inference of sex chromosome karyotypes and sex-linked\nscaffolds from low-depth sequencing data.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 10:12:56 UTC", "User": "root" }, "Author": "Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph\nLeuenberger [ctb], Daniel Wegmann [aut]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2024-08-24 02:46:56 UTC", "RemoteUrl": "https://github.com/cran/bexy", "RemoteRef": "HEAD", "RemoteSha": "96d2546ca9187106e3a7a244ee9f0e41225706b2", "MD5sum": "a4aba2347b96ada47928f2cb77a372d2", "_user": "cran", "_type": "src", "_file": "bexy_0.1.3.tar.gz", "_fileid": "3c7208a7a2c04ae321030896c78572ab418a1ef965ff7690eaa5ac91df657c04", "_filesize": 154867, "_sha256": "3c7208a7a2c04ae321030896c78572ab418a1ef965ff7690eaa5ac91df657c04", "_created": "2026-05-26T10:12:56.000Z", "_published": "2026-05-26T10:15:28.513Z", "_distro": "noble", "_jobs": [ { "job": 77853070498, "time": 115, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7214456368" }, { "job": 77853070436, "time": 119, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7214457480" }, { "job": 77852642492, "time": 159, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7214418078" }, { "job": 77853070384, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7214458076" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26446046961", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/bexy", "_commit": { "id": "96d2546ca9187106e3a7a244ee9f0e41225706b2", "author": "Madleina Caduff ", "committer": "cran-robot ", "message": "version 0.1.3\n", "time": 1724467616 }, "_maintainer": { "name": "Madleina Caduff", "email": "madleina.caduff@unifr.ch" }, "_registered": true, "_dependencies": [ { "package": "TeachingDemos", "role": "Imports" }, { "package": "Ternary", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 190, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bexy" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/bexy.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.2", "date": "2023-11-29" }, { "version": "0.1.3", "date": "2024-08-26" } ], "_exports": [ "bexy", "getPosteriorMeanRho", "getPosteriorModeAutosomalTrisomy", "getPosteriorModeScaffoldTypes", "getPosteriorModeSexKaryotypes", "getSamplesWithAutosomalTrisomy", "getSamplesWithThisKaryotype", "getScaffoldsWithThisType", "plot.bexy", "plotAutosomalTrisomy", "plotAutosomalTrisomyCounts", "plotAutosomalTrisomyPosteriorProbabilities", "plotBars", "plotCounts", "plotMCMCTrace", "plotTernary", "print.bexy", "summary.bexy", "writePosteriorModeAutosomalTrisomies", "writePosteriorModeScaffoldTypes", "writePosteriorModeSexKaryotypes" ], "_help": [ { "page": "bexy", "title": "Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data", "topics": [ "bexy" ] }, { "page": "getPosteriorMeanRho", "title": "Getting posterior mean rho (ploidy ratio parameter) for each scaffold", "topics": [ "getPosteriorMeanRho" ] }, { "page": "getPosteriorModeAutosomalTrisomy", "title": "Getting the posterior mode for each autosomal trisomy", "topics": [ "getPosteriorModeAutosomalTrisomy" ] }, { "page": "getPosteriorModeScaffoldTypes", "title": "Getting the posterior mode for each scaffold type", "topics": [ "getPosteriorModeScaffoldTypes" ] }, { "page": "getPosteriorModeSexKaryotypes", "title": "Getting the posterior mode for each sex karyotype", "topics": [ "getPosteriorModeSexKaryotypes" ] }, { "page": "getSamplesWithAutosomalTrisomy", "title": "Getting all samples classified as a certain autosomal trisomy", "topics": [ "getSamplesWithAutosomalTrisomy" ] }, { "page": "getSamplesWithThisKaryotype", "title": "Getting all samples classified as a specific sex karyotype", "topics": [ "getSamplesWithThisKaryotype" ] }, { "page": "getScaffoldsWithThisType", "title": "Getting all scaffolds classified as a specific scaffold type", "topics": [ "getScaffoldsWithThisType" ] }, { "page": "plot.bexy", "title": "Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).", "topics": [ "plot.bexy" ] }, { "page": "plotAutosomalTrisomy", "title": "Plotting the autosomal trisomies", "topics": [ "plotAutosomalTrisomy" ] }, { "page": "plotAutosomalTrisomyCounts", "title": "Plotting the autosomal trisomies: counts on that scaffold", "topics": [ "plotAutosomalTrisomyCounts" ] }, { "page": "plotAutosomalTrisomyPosteriorProbabilities", "title": "Plotting the autosomal trisomies: posterior probabilities", "topics": [ "plotAutosomalTrisomyPosteriorProbabilities" ] }, { "page": "plotBars", "title": "Plotting a barplot with the posterior probabilities of each sex karyotype per sample", "topics": [ "plotBars" ] }, { "page": "plotCounts", "title": "Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype", "topics": [ "plotCounts" ] }, { "page": "plotMCMCTrace", "title": "Plot the MCMC trace for a specific parameter", "topics": [ "plotMCMCTrace" ] }, { "page": "plotTernary", "title": "Plotting the ternary of a bexy object", "topics": [ "plotTernary" ] }, { "page": "print.bexy", "title": "Printing a bexy object", "topics": [ "print.bexy" ] }, { "page": "summary.bexy", "title": "Summarizing a bexy object", "topics": [ "summary.bexy" ] }, { "page": "writePosteriorModeAutosomalTrisomies", "title": "Write a file with the posterior mode for each autosomal trisomy", "topics": [ "writePosteriorModeAutosomalTrisomies" ] }, { "page": "writePosteriorModeScaffoldTypes", "title": "Write a file with the posterior mode for each scaffold type", "topics": [ "writePosteriorModeScaffoldTypes" ] }, { "page": "writePosteriorModeSexKaryotypes", "title": "Write a file with the posterior mode for each sex karyotype", "topics": [ "writePosteriorModeSexKaryotypes" ] } ], "_rundeps": [ "ape", "base64enc", "bit", "bit64", "bslib", "cachem", "cli", "colorspace", "commonmark", "digest", "fastmap", "fastmatch", "fontawesome", "fs", "glue", "htmltools", "httpuv", "jquerylib", "jsonlite", "later", "lattice", "lifecycle", "magrittr", "memoise", "mime", "nlme", "otel", "PlotTools", "promises", "R6", "rappdirs", "rbibutils", "Rcpp", "Rdpack", "rlang", "sass", "shiny", "shinyjs", "sourcetools", "sp", "TeachingDemos", "Ternary", "TreeDist", "TreeTools", "withr", "xtable" ], "_score": 1, "_indexed": true, "_nocasepkg": "bexy", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-05-26T10:14:57.000Z", "distro": "noble", "commit": "96d2546ca9187106e3a7a244ee9f0e41225706b2", "fileid": "cd1066a9ca42b148b39d8d02f3114dc2f9f464a611079f2c6390de9f5ed1dec2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26446046961" }, { "r": "4.6.0", "os": "linux", "version": "0.1.3", "date": "2026-05-26T10:14:57.000Z", "distro": "noble", "commit": "96d2546ca9187106e3a7a244ee9f0e41225706b2", "fileid": "9b4c05005cc44bdf90d18da3ba94cd60e19c7a3f50ad4f642f5783a0d68c1b0e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26446046961" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.3", "date": "2026-05-26T10:15:14.000Z", "commit": "96d2546ca9187106e3a7a244ee9f0e41225706b2", "fileid": "5450b0387a145e6053b13b5db58663344d1d218db96621c72edac85c4e4b34b3", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26446046961" } ] }