{ "_id": "6a194ee1acfb0bcc41ddece8", "Package": "PIPETS", "Title": "Poisson Identification of PEaks from Term-Seq data", "Version": "1.8.0", "Authors@R": "person(\"Quinlan\", \"Furumo\", email=\"furumo@bc.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4486-302X\"))", "Description": "PIPETS provides statistically robust analysis for\n3'-seq/term-seq data. It utilizes a sliding window approach to\napply a Poisson Distribution test to identify genomic positions\nwith termination read coverage that is significantly higher\nthan the surrounding signal. PIPETS then condenses proximal\nsignal and produces strand specific results that contain all\nsignificant termination peaks.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "BugReports": "https://github.com/qfurumo/PIPETS/issues", "URL": "https://github.com/qfurumo/PIPETS", "biocViews": "Sequencing, Transcription, GeneRegulation, PeakDetection,\nGenetics, Transcriptomics, Coverage", "Config/testthat/edition": "3", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:02:18 UTC", "RemoteUrl": "https://github.com/bioc/PIPETS", "RemoteRef": "RELEASE_3_23", "RemoteSha": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:26:10 UTC", "User": "root" }, "Author": "Quinlan Furumo [aut, cre] (ORCID:\n)", "Maintainer": "Quinlan Furumo ", "MD5sum": "a3d03cf2a73d4ba40f45370daffc672b", "_user": "bioc-release", "_type": "src", "_file": "PIPETS_1.8.0.tar.gz", "_fileid": "79f7045bf0c62f5e9f5b2ca819d93d50b23e652815a235ee2b053fd0d894d98f", "_filesize": 2833197, "_sha256": "79f7045bf0c62f5e9f5b2ca819d93d50b23e652815a235ee2b053fd0d894d98f", "_created": "2026-05-29T07:26:10.000Z", "_published": "2026-05-29T08:31:29.433Z", "_jobs": [ { "job": 78456933302, "time": 155, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285405024" }, { "job": 78456933327, "time": 230, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285427076" }, { "job": 78456933296, "time": 212, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285421866" }, { "job": 78456933310, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7286466634" }, { "job": 78456933294, "time": 107, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7286471537" }, { "job": 78456459816, "time": 207, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285357473" }, { "job": 78456933284, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285387308" }, { "job": 78456933319, "time": 130, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285397253" }, { "job": 78456933288, "time": 107, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285390370" }, { "job": 78456933309, "time": 110, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285391698" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PIPETS", "_commit": { "id": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381338 }, "_maintainer": { "name": "Quinlan Furumo", "email": "furumo@bc.edu", "orcid": "0000-0003-4486-302X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "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": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "transcription", "generegulation", "peakdetection", "genetics", "transcriptomics", "coverage" ], "_stars": 0, "_contributors": [ { "user": "qfurumo", "count": 36, "uuid": 33698007 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 268, "source": "https://www.bioconductor.org/packages/stats/bioc/PIPETS" }, "_devurl": "https://github.com/qfurumo/pipets", "_searchresults": 4, "_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/PIPETS.html", "manual.pdf" ], "_homeurl": "https://github.com/qfurumo/pipets", "_realowner": "bioc", "_cranurl": false, "_exports": [ "PIPETS_FullRun" ], "_help": [ { "page": "PIPETS_FullRun", "title": "Analyze 3'-seq Data with PIPETS Poisson Identification of PEaks from Term-Seq data. This is the full run method that begins with input Bed file and returns the strand split results", "topics": [ "PIPETS_FullRun" ] } ], "_rundeps": [ "BiocGenerics", "cli", "dplyr", "generics", "GenomicRanges", "glue", "IRanges", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "rlang", "S4Vectors", "Seqinfo", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "PIPETS.Rmd", "filename": "PIPETS.html", "title": "Analyzing 3'-seq/Term-seq Data with PIPETS", "author": "Author: Quinlan Furumo", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick Start", "Installation", "Basic PIPETS Run", "Bed File Input", "GRanges Object Input", "Bed File Input and Strand Specific Analysis", "PIPETS Output", "Detailed Walkthrough", "Input Data Specifications", "Method Steps", "Step One: Poisson Test to Identify Significant Positions", "Step Two: Condensing of Proximal Significant Positions", "Step Three: Condensing of Proximal Significant Peaks", "Other Parameters", "slidingWindowSize", "slidingWindowMovementDistance", "adjacentPeakDistance", "peakCondensingDistance", "threshAdjust", "user_pValue", "highOutlierTrim", "inputDataFormat", "Session Info" ], "created": "2023-09-25 19:57:10", "modified": "2024-09-30 18:15:11", "commits": 15 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "pipets", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/PIPETS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-05-29T07:29:28.000Z", "distro": "noble", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "8ef63ab5326ba5727332d38110df41407829f08b5f218606e296c822a9da0f15", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0", "date": "2026-05-29T07:29:13.000Z", "distro": "noble", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "b8d21cfd8579320ce7316d3b40fa81404445587dc4adc5f340c5ee9fceeed2ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-05-29T08:30:25.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "2a49790191ce4262e041d56e73cf73879d7f81013c87e76fd5e17a9a6a81602b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0", "date": "2026-05-29T08:30:40.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "219acdece10a32f05e50472d26de9c1c22b5dcc02a4bb143a38858ea8602e2af", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-05-29T07:28:08.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "49e84b88d5db9b567d4fdaf8ad37dc95816fa3217925b3e9727901e88956f4f6", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-05-29T07:27:46.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "2810c09b38b2e908330674e5b0c612b6035c777bba1fb4ca86aa2e7a6f454ab3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-05-29T07:27:24.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "35a08a3afd2cef9db4ffe89dce0e2ef839f27d2eae218cca110b8bba5d7d417d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" }, { "r": "4.6.0", "os": "win", "version": "1.8.0", "date": "2026-05-29T07:27:27.000Z", "commit": "ea66b69e80f1bfdf4ac0ab72e6e6ae3ef47726aa", "fileid": "0498e9725d44cb855e479a5d4a6589f1c3da3e14433c27f84a0cf80ffd07db61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624043383" } ] }