{ "_id": "6a1e9e311d7bb097a0a6fad0", "Type": "Package", "Package": "locuscomparer", "Title": "locuscomparer: Visualization of GWAS-QTL Colocalization Events", "Version": "1.0.0", "Authors@R": "c(\nperson(\"Boxiang\", \"Liu\", , \"jollier.liu@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Michael\", \"Gloudemans\", , \"mgloud@stanford.edu\", role = \"ctb\"),\nperson(\"Stephen\", \"Montgomery\", , \"smontgom@stanford.edu\", role = \"ctb\")\n)", "Description": "locuscomparer is the standalone version of the\nLocusCompare webserver (www.locuscompare.ml:3838).\nlocuscomparer performs visualization of colocalization of\nsummary statistics from pairs of association datasets (e.g.\nGWAS and eQTL).", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libmysqlclient-dev", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2025-08-06 08:01:56 UTC", "RemoteUrl": "https://github.com/remlapmot/locuscomparer", "RemoteRef": "suggestions", "RemoteSha": "208d7fae39096ec599e940faee9c9fc31f450085", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 09:08:11 UTC", "User": "root" }, "Author": "Boxiang Liu [aut, cre],\nMichael Gloudemans [ctb],\nStephen Montgomery [ctb]", "Maintainer": "Boxiang Liu ", "MD5sum": "ff9d274dc98453749d13bb15744000c7", "_user": "mrcieu", "_type": "src", "_file": "locuscomparer_1.0.0.tar.gz", "_fileid": "8e837e71faa8532fb951b261d4dbaa1f7d5c19abcc7c2e0ed11ca1c1f1dcd2a9", "_filesize": 218396, "_sha256": "8e837e71faa8532fb951b261d4dbaa1f7d5c19abcc7c2e0ed11ca1c1f1dcd2a9", "_created": "2026-06-02T09:08:11.000Z", "_published": "2026-06-02T09:11:13.824Z", "_distro": "noble", "_jobs": [ { "job": 79037117922, "time": 143, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7353586025" }, { "job": 79037118010, "time": 133, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7353582429" }, { "job": 79037117898, "time": 140, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7353584288" }, { "job": 79037117825, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7353572045" }, { "job": 79036741794, "time": 132, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7353534412" }, { "job": 79037117811, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353573425" }, { "job": 79037117962, "time": 97, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7353569870" }, { "job": 79037118184, "time": 69, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7353560114" }, { "job": 79037118018, "time": 76, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7353562444" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/remlapmot/locuscomparer", "_commit": { "id": "208d7fae39096ec599e940faee9c9fc31f450085", "author": "Tom Palmer ", "committer": "Tom Palmer ", "message": "Add helpfile for dataset\n", "time": 1754467316 }, "_maintainer": { "name": "Boxiang Liu", "email": "jollier.liu@gmail.com", "login": "boxiangliu", "bluesky": "@boxiangliu.bsky.social", "linkedin": "in/boxiang", "twitter": "@boxiangliu", "description": "Presidential Young Professor @nus, Staff Research Scientist @baidu, Ph.D. @Stanford. Working in the intersection between AI/ML and biology/medicine. ", "uuid": 4122434 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "cowplot", "version": ">= 0.6.1", "role": "Imports" }, { "package": "DBI", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 2.2.1", "role": "Imports" }, { "package": "ggrepel", "version": ">= 0.6.5", "role": "Imports" }, { "package": "RMySQL", "version": ">= 0.10.17", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "remlapmot", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-32", "n": 28 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "boxiangliu", "count": 37, "uuid": 4122434 }, { "user": "mikegloudemans", "count": 1, "uuid": 3655881 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/locuscomparer" }, "_devurl": "https://github.com/remlapmot/locuscomparer", "_searchresults": 125, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/locuscomparer.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_label", "assign_color", "get_lead_snp", "get_position", "locuscompare", "make_combined_plot", "make_locuszoom", "make_scatterplot", "read_metal", "retrieve_LD" ], "_datasets": [ { "name": "config", "title": "Example dataset", "object": "config", "class": [ "data.frame" ], "fields": [ "a", "b", "c" ], "rows": 1, "table": true, "tojson": true } ], "_help": [ { "page": "add_label", "title": "Add a column of SNP labels to input data.frame", "topics": [ "add_label" ] }, { "page": "assign_color", "title": "Assign color to each SNP according to LD.", "topics": [ "assign_color" ] }, { "page": "config", "title": "Example dataset", "topics": [ "config" ] }, { "page": "get_lead_snp", "title": "Get the lead SNP from the list of SNPs in input data.frame The lead SNP is defined as the SNP with the lowest sum of p-values from the two studies.", "topics": [ "get_lead_snp" ] }, { "page": "get_position", "title": "Append two columns, chromosome (chr) and position (pos), to the input data.frame.", "topics": [ "get_position" ] }, { "page": "locuscompare", "title": "Make a locuscompare plot.", "topics": [ "locuscompare" ] }, { "page": "make_combined_plot", "title": "Generated a combined plot with two locuszoom plots and a locuscompare plot. Each locuszoom plot represent an association study.", "topics": [ "make_combined_plot" ] }, { "page": "make_locuszoom", "title": "Make a locuszoom plot. Details see http://locuszoom.org/.", "topics": [ "make_locuszoom" ] }, { "page": "make_scatterplot", "title": "Make a scatter plot (called the LocusCompare plot). Each axis of the LocusCompare plot represent the -log10(p-value) from an association study. Each point thus represent a SNP. By default, the lead SNP is a purple diamond, whereas the other SNPs are colored according to their LD with the lead SNP.", "topics": [ "make_scatterplot" ] }, { "page": "read_metal", "title": "Read association summary statistics from file and append column. The file must contain 2 columns: markers, i.e SNPs, and p-value. The marker column should contain SNP rsIDs.", "topics": [ "read_metal" ] }, { "page": "retrieve_LD", "title": "Retrive SNP pairwise LD from database. SNP pairwise lD are calculated based on 1000 Genomes Project Phase 3 version 5. For storage-efficiency, the output will only include SNPs with r2 > 0.2 with the input SNP.", "topics": [ "retrieve_LD" ] } ], "_readme": "https://github.com/remlapmot/locuscomparer/raw/suggestions/README.md", "_rundeps": [ "cli", "cowplot", "cpp11", "DBI", "farver", "ggplot2", "ggrepel", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "Rcpp", "rlang", "RMySQL", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 2.795880017344075, "_indexed": false, "_nocasepkg": "locuscomparer", "_universes": [ "mrcieu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-02T09:10:27.000Z", "distro": "noble", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "634335c929fc1066208243f83d63b47535e4fe2d98aac4f5dcdcda2249c29b5a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-02T09:10:17.000Z", "distro": "noble", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "ef5a300ac57ba2ac6735a3366557b3d1f5da9dafd472fdfbbb2d938267d4f0e4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-02T09:10:27.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "780452319c6e01b92a46cd80882ae6b4ed5f8185c03eb4b73fc3626afa1bb67f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-02T09:09:48.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "34669aa5277bcfea6c9af20312f6b633cd45b55d31b8804e0a38a523ddcba74f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-02T09:10:14.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "a9462ce4a3f3aab2f02363bfdcccc0b1eafb3600c94bf4bcd83c1bfd60c2f2c8", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-06-02T09:09:36.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "f93955a34e8f23b52c198d037d8e48194dd927cf0402784ef0065ab03d6bf62d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-06-02T09:09:16.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "081e9eb346129ccd9fb2ef75a2f9676541773f7a4000991b14b902d7eae58acf", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-06-02T09:09:12.000Z", "commit": "208d7fae39096ec599e940faee9c9fc31f450085", "fileid": "10962343efbb56afdbc755f965e576703a6dd85a5a9406f7f75be5b0a87eb53f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26809850157" } ] }