{ "_id": "6a1acda01d7bb097a09df43b", "Package": "ggmanh", "Title": "Visualization Tool for GWAS Result", "Version": "1.17.0", "Authors@R": "c(\nperson(given = \"John\", family = \"Lee\", role = c(\"aut\", \"cre\"), email = \"swannyy.stat@gmail.com\"),\nperson(given = \"John\", family = \"Lee\", role = c(\"aut\"), email = \"john.lee@abbvie.com\", comment = \"AbbVie\"),\nperson(given = \"Xiuwen\", family = \"Zheng\", role = c(\"ctb\", \"dtc\"), email = \"xiuwen.zheng@abbvie.com\")\n)", "Description": "Manhattan plot and QQ Plot are commonly used to visualize\nthe end result of Genome Wide Association Study. The \"ggmanh\"\npackage aims to keep the generation of these plots simple while\nmaintaining customizability. Main functions include\nmanhattan_plot, qqunif, and thinPoints.", "biocViews": "Visualization, GenomeWideAssociation, Genetics", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:32 UTC", "RemoteUrl": "https://github.com/bioc/ggmanh", "RemoteRef": "HEAD", "RemoteSha": "43f0523906771d73edeaa11f0af866a8ebca69ad", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:10:45 UTC", "User": "root" }, "Author": "John Lee [aut, cre],\nJohn Lee [aut] (AbbVie),\nXiuwen Zheng [ctb, dtc]", "Maintainer": "John Lee ", "MD5sum": "1f21ef5f82e9e2d78fcce57b98eb4800", "_user": "bioc", "_type": "src", "_file": "ggmanh_1.17.0.tar.gz", "_fileid": "e0902bafefea655f361ed0818d39ec7f30153cd1c1fc3f7fa432f3e0d4172d43", "_filesize": 4313111, "_sha256": "e0902bafefea655f361ed0818d39ec7f30153cd1c1fc3f7fa432f3e0d4172d43", "_created": "2026-05-30T08:10:45.000Z", "_published": "2026-05-30T11:44:32.407Z", "_jobs": [ { "job": 78635706946, "time": 159, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306743081" }, { "job": 78635706943, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306747204" }, { "job": 78635706934, "time": 176, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306744733" }, { "job": 78635706970, "time": 137, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307931086" }, { "job": 78635706951, "time": 108, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307927764" }, { "job": 78635497303, "time": 249, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306727040" }, { "job": 78635706940, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306739343" }, { "job": 78635706959, "time": 98, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306737569" }, { "job": 78635706948, "time": 92, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306736873" }, { "job": 78635706971, "time": 113, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306738882" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ggmanh", "_commit": { "id": "43f0523906771d73edeaa11f0af866a8ebca69ad", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381052 }, "_maintainer": { "name": "John Lee", "email": "swannyy.stat@gmail.com", "login": "swannyy14", "description": "Mathematics & Statistics Major.\nHi :)", "uuid": 28781474 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "gdsfmt", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "paletteer", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "SeqArray", "version": ">= 1.32.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "pals", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "visualization", "genomewideassociation", "genetics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 406, "source": "https://www.bioconductor.org/packages/stats/bioc/ggmanh" }, "_searchresults": 43, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ggmanh.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "binned_manhattan_plot", "binned_manhattan_preprocess", "calc_new_pos", "default_gds_path", "gds_annotate", "manhattan_data_preprocess", "manhattan_plot", "manhattan_plot.default", "qqunif", "thinPoints" ], "_help": [ { "page": "binned_manhattan_plot", "title": "Plot Binned Manhattan Plot", "topics": [ "binned_manhattan_plot", "binned_manhattan_plot,GRanges-method", "binned_manhattan_plot.data.frame", "binned_manhattan_plot.default", "binned_manhattan_plot.MPdataBinned" ] }, { "page": "binned_manhattan_preprocess", "title": "Preprocess GWAS Result for Binned Manhattan Plot", "topics": [ "binned_manhattan_preprocess", "binned_manhattan_preprocess,GRanges-method", "binned_manhattan_preprocess.data.frame", "binned_manhattan_preprocess.default", "binned_manhattan_preprocess.MPdata" ] }, { "page": "calc_new_pos", "title": "Calculate new x-position of each point", "topics": [ "calc_new_pos" ] }, { "page": "default_gds_path", "title": "Path to Default GDS File", "topics": [ "default_gds_path" ] }, { "page": "gds_annotate", "title": "Annotation with GDS File", "topics": [ "gds_annotate" ] }, { "page": "ggmanh", "title": "ggmanh: A package for visualization of GWAS results.", "topics": [ "ggmanh" ] }, { "page": "ggmanh_annotation_gds", "title": "gnomAD Variant Annotation in SeqArray Format", "topics": [ "ggmanh_annotation_gds" ] }, { "page": "manhattan_data_preprocess", "title": "Preprocess GWAS Result", "topics": [ "manhattan_data_preprocess", "manhattan_data_preprocess,GRanges-method", "manhattan_data_preprocess.data.frame", "manhattan_data_preprocess.default" ] }, { "page": "manhattan_plot", "title": "Manhattan Plotting", "topics": [ "manhattan_plot", "manhattan_plot,GRanges-method", "manhattan_plot.data.frame", "manhattan_plot.default", "manhattan_plot.MPdata" ] }, { "page": "qqunif", "title": "Plot Quantile-Quantile Plot of p-values against uniform distribution.", "topics": [ "qqunif" ] }, { "page": "thinPoints", "title": "Thin Data Points", "topics": [ "thinPoints" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "cli", "colorspace", "cpp11", "crayon", "dichromat", "digest", "dplyr", "farver", "gdsfmt", "generics", "GenomicRanges", "ggplot2", "ggrepel", "glue", "gtable", "IRanges", "isoband", "labeling", "lifecycle", "magrittr", "mapproj", "maps", "paletteer", "pals", "pillar", "pkgconfig", "prismatic", "purrr", "R6", "RColorBrewer", "Rcpp", "rematch2", "rlang", "rstudioapi", "S4Vectors", "S7", "scales", "SeqArray", "Seqinfo", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "ggmanh.Rmd", "filename": "ggmanh.html", "title": "Guide to ggmanh Package", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Functions Overview", "Example with Simulated GWAS", "Rescaling", "Annotation", "Highlighting", "thinPoints", "Zoom into Chromosome", "Binned Manhattan Plot", "Choosing Palettes for Coloring Bins", "Summary Expression", "Annotation with GDS File", "SessionInfo" ], "created": "2021-09-01 19:23:00", "modified": "2024-09-19 03:03:34", "commits": 13 } ], "_score": 3.934498451243568, "_indexed": true, "_nocasepkg": "ggmanh", "_universes": [ "bioc", "swannyy14" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:14:01.000Z", "distro": "noble", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "b352df81e7df2c8693aad39007f36b0647018b3b068d079fc7b44a7f40a8cb66", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:13:33.000Z", "distro": "noble", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "102d1c09652111c78cf4a9476761aef84678f10e035a27f181398b412abfc396", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:43:36.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "4958c1ceaeaf38261f062a42fd37a0fbd0d902ba217dd811a32781c404ead882", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.6.0", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:43:02.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "f1a26c51478a90dbbe9b0d539b4954f562571959fd879968578f5cc7ba678c5b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-05-30T08:13:08.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "dba51e8c149c85a60e41194fdf291e889a63cd865a117ea147aa5908df50369f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:12:11.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "f612e511720afcf207929ac0a26666058e7ca771f67ec10daa0ed10a0d7327d1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:12:03.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "73325f4f63b17f733ff14cfd1d4358995a6277aa7d867203bbd8fc05594f0234", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" }, { "r": "4.6.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:12:18.000Z", "commit": "43f0523906771d73edeaa11f0af866a8ebca69ad", "fileid": "46e75b3fd26b2f6f8760c191c0330bf3f8d13a2c5ef281ced9111981e174d38d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678825762" } ] }