{ "_id": "6a1af4b31d7bb097a09f8d42", "Package": "seq.hotSPOT", "Type": "Package", "Title": "Targeted sequencing panel design based on mutation hotspots", "Version": "1.13.0", "Authors@R": "c(\nperson(\"Sydney\", \"Grant\", email = \"sydney.grant@roswellpark.org\", role = c(\"aut\", \"cre\")),\nperson(\"Lei\", \"Wei\", email = \"lei.wei@roswellpark.org\", role = c(\"aut\")),\nperson(\"Gyorgy\", \"Paragh\", email = \"gyorgy.paragh@roswellpark.org\", role = c(\"aut\")))", "Description": "seq.hotSPOT provides a resource for designing effective\nsequencing panels to help improve mutation capture efficacy for\nultradeep sequencing projects. Using SNV datasets, this package\ndesigns custom panels for any tissue of interest and identify\nthe genomic regions likely to contain the most mutations.\nEstablishing efficient targeted sequencing panels can allow\nresearchers to study mutation burden in tissues at high depth\nwithout the economic burden of whole-exome or whole-genome\nsequencing. This tool was developed to make high-depth\nsequencing panels to study low-frequency clonal mutations in\nclinically normal and cancerous tissues.", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "FALSE", "RoxygenNote": "7.2.3", "biocViews": "Software, Technology, Sequencing, DNASeq, WholeGenome", "VignetteBuilder": "knitr", "URL": "https://github.com/sydney-grant/seq.hotSPOT", "BugReports": "https://github.com/sydney-grant/seq.hotSPOT/issues", "Config/testthat/edition": "3", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:32 UTC", "RemoteUrl": "https://github.com/bioc/seq.hotSPOT", "RemoteRef": "HEAD", "RemoteSha": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:46:24 UTC", "User": "root" }, "Author": "Sydney Grant [aut, cre],\nLei Wei [aut],\nGyorgy Paragh [aut]", "Maintainer": "Sydney Grant ", "MD5sum": "9cfc79ff5f24baaecb659c7d766963ae", "_user": "bioc", "_type": "src", "_file": "seq.hotSPOT_1.13.0.tar.gz", "_fileid": "07ebb84475fbfee2306d98be9aa89e73fb4ea4372ab28ce7807809cd252537ae", "_filesize": 1351065, "_sha256": "07ebb84475fbfee2306d98be9aa89e73fb4ea4372ab28ce7807809cd252537ae", "_created": "2026-05-30T09:46:24.000Z", "_published": "2026-05-30T14:31:14.980Z", "_jobs": [ { "job": 78640584902, "time": 139, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307473849" }, { "job": 78640584903, "time": 168, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307475985" }, { "job": 78640584905, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307477136" }, { "job": 78640584909, "time": 127, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308884685" }, { "job": 78640584919, "time": 100, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308882116" }, { "job": 78639929550, "time": 175, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307285718" }, { "job": 78640584901, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307470372" }, { "job": 78640584908, "time": 83, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307467663" }, { "job": 78640584912, "time": 82, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307469391" }, { "job": 78640584911, "time": 81, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307467378" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/seq.hotSPOT", "_commit": { "id": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381232 }, "_maintainer": { "name": "Sydney Grant", "email": "sydney.grant@roswellpark.org" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "R.utils", "role": "Imports" }, { "package": "hash", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "base", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "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" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23" } ], "_topics": [ "software", "technology", "sequencing", "dnaseq", "wholegenome" ], "_stars": 0, "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 264, "source": "https://www.bioconductor.org/packages/stats/bioc/seq.hotSPOT" }, "_devurl": "https://github.com/sydney-grant/seq.hotspot", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/seq.hotSPOT.html", "manual.pdf" ], "_homeurl": "https://github.com/sydney-grant/seq.hotspot", "_realowner": "bioc", "_cranurl": false, "_exports": [ "amp_pool", "com_hotspot", "fw_hotspot" ], "_datasets": [ { "name": "mutation_data", "title": "Single Nucleotide Variants in Clinically-Normal Epidermis", "object": "mutation_data", "file": "mutation_data.RData", "class": [ "data.frame" ], "fields": [ "chr", "pos", "gene" ], "rows": 201, "table": true, "tojson": true } ], "_help": [ { "page": "amp_pool", "title": "create amplicon pool", "topics": [ "amp_pool" ] }, { "page": "com_hotspot", "title": "comprehensive amplicon ranking", "topics": [ "com_hotspot" ] }, { "page": "fw_hotspot", "title": "forward amplicon ranking", "topics": [ "fw_hotspot" ] }, { "page": "mutation_data", "title": "Single Nucleotide Variants in Clinically-Normal Epidermis", "topics": [ "mutation_data" ] }, { "page": "seq.hotSPOT", "title": "Targeted sequencing panel design based on mutation hotspots", "topics": [ "seq.hotSPOT" ] } ], "_readme": "https://github.com/bioc/seq.hotSPOT/raw/HEAD/README.md", "_rundeps": [ "hash", "R.methodsS3", "R.oo", "R.utils" ], "_vignettes": [ { "source": "hotSPOT-vignette.Rmd", "filename": "hotSPOT-vignette.html", "title": "hotSPOT-vignette", "author": "Sydney Grant, Lei Wei, Gyorgy Paragh", "engine": "knitr::rmarkdown", "headings": [ "seq.hotSPOT", "Sydney R. Grant^1,2^, Lei Wei^3^, Gyorgy Paragh^1,2^", "Introduction", "Installation & Setup", "Generation of Amplicon Pool", "Dataset", "amp_pool", "Forward Selection Sequencing Panel Identifier", "fw_hotspot", "Comprehensive Selection Sequencing Panel Identifier", "com_hotspot" ], "created": "2023-03-08 22:39:38", "modified": "2023-04-11 17:22:14", "commits": 6 } ], "_score": 4, "_indexed": true, "_nocasepkg": "seq.hotspot", "_universes": [ "bioc", "sydney-grant" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.0", "date": "2026-05-30T10:20:24.000Z", "distro": "noble", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "732f6bcecabbc9908a55dcfc43720c55c98a777a2120936569cf90d1451106d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.6.0", "os": "linux", "version": "1.13.0", "date": "2026-05-30T10:20:37.000Z", "distro": "noble", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "400aab9d1d6b4a84954f4b4cf89fe3870db4db82d09ec4bf0222b64400eb02f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.5.3", "os": "mac", "version": "1.13.0", "date": "2026-05-30T14:30:38.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "829c989a590987ba738308e8cbff0a62a9633ea6b7cd431c028dc83625bc0d14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.6.0", "os": "mac", "version": "1.13.0", "date": "2026-05-30T14:30:22.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "e32c3b5ed9dc6abe20ccc8c734ef41ccf6e71af7423fabb4b76b94b25d69347a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.0", "date": "2026-05-30T10:19:42.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "2abfc126be59848d93880c57ef4c6fdf13ca93b0ebc5d380121349e0755a2509", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.7.0", "os": "win", "version": "1.13.0", "date": "2026-05-30T10:18:48.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "820293253ea29070f01f725fe615048e654619bdc03b12e04db0debc225e16ac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.5.3", "os": "win", "version": "1.13.0", "date": "2026-05-30T10:19:05.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "e0c484ba39ba3b645478aafd9397402eec1299c1a2255e0460f55b046410ee5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" }, { "r": "4.6.0", "os": "win", "version": "1.13.0", "date": "2026-05-30T10:18:40.000Z", "commit": "c885a57b3cb92b12f78bc31d37e8945718f95c4a", "fileid": "3fbb733ec7abdd18d7545d959db89c1c3f94e5d2fc687cd445f21b25d2619a07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677054274" } ] }