{ "_id": "6ac6514df511ae58c09aa042", "Package": "EDIRquery", "Title": "Query the EDIR Database For Specific Gene", "Version": "1.13.0", "Authors@R": "person(\"Laura D.T.\", \"Vo Ngoc\", , \"doan.vongoc@vub.be\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1597-900X\"))", "Description": "EDIRquery provides a tool to search for genes of interest\nwithin the Exome Database of Interspersed Repeats (EDIR). A\ngene name is a required input, and users can additionally\nspecify repeat sequence lengths, minimum and maximum distance\nbetween sequences, and whether to allow a 1-bp mismatch.\nOutputs include a summary of results by repeat length, as well\nas a dataframe of query results. Example data provided includes\na subset of the data for the gene GAA (ENSG00000171298). To\nquery the full database requires providing a path to the\ndownloaded database files as a parameter.", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "Genetics, SequenceMatching", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:33 UTC", "RemoteUrl": "https://github.com/bioc/EDIRquery", "RemoteRef": "HEAD", "RemoteSha": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-07 11:22:40 UTC", "User": "root" }, "Author": "Laura D.T. Vo Ngoc [aut, cre] (ORCID:\n)", "Maintainer": "Laura D.T. Vo Ngoc ", "_user": "bioc", "_type": "src", "_file": "EDIRquery_1.13.0.tar.gz", "_fileid": "https://r2.ropensci.org/26199afee7ff5e49eaec0af9a903a867e1d013fc574b8b3d07cd0d958f093b6f", "_filesize": 1320741, "_sha256": "26199afee7ff5e49eaec0af9a903a867e1d013fc574b8b3d07cd0d958f093b6f", "_expires": "2027-01-15T14:03:55.000Z", "_created": "2026-10-07T11:22:40.000Z", "_published": "2026-10-07T14:03:57.339Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_upstream": "https://github.com/bioc/EDIRquery", "_commit": { "id": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381233 }, "_maintainer": { "name": "Laura D.T. Vo Ngoc", "email": "doan.vongoc@vub.be", "login": "lauravongoc", "description": "", "uuid": 36701599, "orcid": "0000-0002-1597-900X" }, "_distro": "resolute", "_jobs": [ { "job": 112766956246, "time": 168, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11479706674" }, { "job": 112766956441, "time": 284, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11478832129" }, { "job": 112766956371, "time": 330, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11478847305" }, { "job": 112766956521, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11487317880" }, { "job": 112766956515, "time": 203, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11486673420" }, { "job": 112765503583, "time": 226, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11479745912" }, { "job": 112766956280, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11479031953" }, { "job": 112766956326, "time": 213, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11479282056" }, { "job": 112766956541, "time": 189, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11479396844" }, { "job": 112766956369, "time": 184, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11479546774" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "tibble", "version": ">= 3.1.6", "role": "Imports" }, { "package": "tictoc", "version": ">= 1.0.1", "role": "Imports" }, { "package": "utils", "version": ">= 4.1.3", "role": "Imports" }, { "package": "stats", "version": ">= 4.1.3", "role": "Imports" }, { "package": "readr", "version": ">= 2.1.2", "role": "Imports" }, { "package": "InteractionSet", "version": ">= 1.22.0", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.46.1", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "genetics", "sequencematching" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 473, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 304, "source": "https://www.bioconductor.org/packages/stats/bioc/EDIRquery" }, "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EDIRquery.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "gene_lookup" ], "_datasets": [ { "name": "gene_chr", "title": "Gene chromosome location", "object": "gene_chr", "file": "gene_chr.rda", "class": [ "data.frame" ], "fields": [ "chromosome_name", "ensembl_gene_id", "hgnc_symbol" ], "rows": 60571, "table": true, "tojson": true } ], "_help": [ { "page": "gene_chr", "title": "Gene chromosome location", "topics": [ "gene_chr" ] }, { "page": "gene_lookup", "title": "Look Up a Gene in EDIR Dataset", "topics": [ "gene_lookup" ] } ], "_readme": "https://github.com/bioc/EDIRquery/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "DelayedArray", "generics", "GenomicRanges", "glue", "hms", "InteractionSet", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "Rcpp", "readr", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "tibble", "tictoc", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr", "XVector" ], "_vignettes": [ { "source": "EDIRquery.Rmd", "filename": "EDIRquery.html", "title": "EDIRquery", "author": "Laura D.T. Vo Ngoc", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Dataset", "Usage", "Installation", "Examples", "Session info" ], "created": "2022-08-30 03:20:42", "modified": "2023-01-16 04:53:01", "commits": 6 } ], "_score": 4, "_indexed": true, "_nocasepkg": "edirquery", "_universes": [ "bioc", "lauravongoc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.0", "date": "2026-10-07T11:25:38.000Z", "distro": "resolute", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/9f447c9418eb71a4e442026c793876e9ca4fa75af4bd372ee1138318762efbf9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.6.1", "os": "linux", "version": "1.13.0", "date": "2026-10-07T11:26:45.000Z", "distro": "resolute", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/3f38d12739bc6d17cadb2f726d131037010e552a6f418f73bb99735658587483", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.5.3", "os": "mac", "version": "1.13.0", "date": "2026-10-07T14:01:32.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/88cb6fe0edbcd972c98dcb5f70dcffa1061bbb51fa796f096374f29522034dfb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.6.1", "os": "mac", "version": "1.13.0", "date": "2026-10-07T14:00:49.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/f2ed90dd7bb2d7b9fcbb59ac7d946d9c16e1c7b2c8708f45557bd22ae2df8328", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.0", "date": "2026-10-07T11:25:12.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/b23e419a9911bdfe2ed74349ef18541840e826ea9c57b91012687b52a6a7f9de", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.7.0", "os": "win", "version": "1.13.0", "date": "2026-10-07T11:24:22.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/2dc7b79fb92940423d570e45874aa984f09a6604a4b9442b24c9f909f7045be4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.5.3", "os": "win", "version": "1.13.0", "date": "2026-10-07T11:24:15.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/8d290d4858a9fd8e3b5d8ebd6fd6551dd7e362a0a37ada9c09afe9825c901331", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" }, { "r": "4.6.1", "os": "win", "version": "1.13.0", "date": "2026-10-07T11:24:14.000Z", "commit": "c3bebae42bf0a3d5140d81a79eaaefafc6e10958", "fileid": "https://r2.ropensci.org/86890cbd8bfe0adb120958181293031498fb1b2993115f8e948dc742b2ead787", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37613251759" } ] }