{ "_id": "6a1af4d91d7bb097a09f8dff", "Type": "Package", "Package": "SMAD", "Title": "Statistical Modelling of AP-MS Data (SMAD)", "Version": "1.29.0", "Authors@R": "person(\"Qingzhou\", \"Zhang\", , \"zqzneptune@hotmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9540-2624\"))", "Description": "Assigning probability scores to protein interactions\ncaptured in affinity purification mass spectrometry (AP-MS)\nexpriments to infer protein-protein interactions. The output\nwould facilitate non-specific background removal as\ncontaminants are commonly found in AP-MS data.", "License": "MIT + file LICENSE", "URL": "https://github.com/zqzneptune/SMAD", "BugReports": "https://github.com/zqzneptune/SMAD/issues", "VignetteBuilder": "knitr", "biocViews": "MassSpectrometry, Proteomics, Software", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libgmp3-dev libicu-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:29 UTC", "RemoteUrl": "https://github.com/bioc/SMAD", "RemoteRef": "HEAD", "RemoteSha": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 09:46:25 UTC", "User": "root" }, "Author": "Qingzhou Zhang [aut, cre] (ORCID:\n)", "Maintainer": "Qingzhou Zhang ", "MD5sum": "bb6ba4faec684a13ca7f7aa40a5db6c6", "_user": "bioc", "_type": "src", "_file": "SMAD_1.29.0.tar.gz", "_fileid": "2c06825078d1916702076da084cd1cd773562f52dacfe4f898843712fdadbbfd", "_filesize": 266513, "_sha256": "2c06825078d1916702076da084cd1cd773562f52dacfe4f898843712fdadbbfd", "_created": "2026-05-30T09:46:25.000Z", "_published": "2026-05-30T14:31:53.717Z", "_jobs": [ { "job": 78640590887, "time": 164, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307477348" }, { "job": 78640590921, "time": 194, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7307305751" }, { "job": 78640590915, "time": 194, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307480085" }, { "job": 78640590908, "time": 161, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307302580" }, { "job": 78640590923, "time": 184, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307479084" }, { "job": 78640590931, "time": 91, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308887020" }, { "job": 78640590942, "time": 244, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7307419921" }, { "job": 78640590927, "time": 107, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308888811" }, { "job": 78640590920, "time": 249, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307419528" }, { "job": 78639924085, "time": 187, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307286449" }, { "job": 78640590888, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307473048" }, { "job": 78640590896, "time": 140, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307475877" }, { "job": 78640590894, "time": 134, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307475313" }, { "job": 78640590910, "time": 134, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307474038" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SMAD", "_commit": { "id": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380569 }, "_maintainer": { "name": "Qingzhou Zhang", "email": "zqzneptune@hotmail.com", "login": "zqzneptune", "twitter": "@QingzhouZ78967", "description": "Architecting Predictive Biology", "uuid": 5545472, "orcid": "0000-0001-9540-2624" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "version": ">= 1.5", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "RcppAlgos", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-15", "n": 1 }, { "week": "2026-17", "n": 9 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "massspectrometry", "proteomics", "software", "cpp" ], "_stars": 0, "_contributors": [ { "user": "zqzneptune", "count": 81, "uuid": 5545472 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "heckendorfc", "count": 1, "uuid": 684117 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 320, "source": "https://www.bioconductor.org/packages/stats/bioc/SMAD" }, "_mentions": 4, "_devurl": "https://github.com/zqzneptune/smad", "_searchresults": 5, "_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/SMAD.html", "manual.pdf" ], "_homeurl": "https://github.com/zqzneptune/smad", "_realowner": "bioc", "_cranurl": false, "_exports": [ "CompPASS", "DICE", "Hart", "HG", "PE" ], "_datasets": [ { "name": "TestDatInput", "title": "Test data for SMAD", "object": "TestDatInput", "file": "TestDatInput.RData", "class": [ "data.frame" ], "fields": [ "idRun", "idBait", "idPrey", "countPrey", "lenPrey" ], "rows": 5000, "table": true, "tojson": true } ], "_help": [ { "page": "CompPASS", "title": "CompPASS", "topics": [ "CompPASS" ] }, { "page": "DICE", "title": "DICE", "topics": [ "DICE" ] }, { "page": "Hart", "title": "Hart", "topics": [ "Hart" ] }, { "page": "HG", "title": "HGScore", "topics": [ "HG" ] }, { "page": "PE", "title": "PE", "topics": [ "PE" ] }, { "page": "TestDatInput", "title": "Test data for SMAD", "topics": [ "TestDatInput" ] } ], "_readme": "https://github.com/bioc/SMAD/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "data.table", "dplyr", "generics", "glue", "gmp", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "Rcpp", "RcppAlgos", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "quickstart.Rmd", "filename": "quickstart.html", "title": "SMAD Quick Start", "author": "Qingzhou Zhang", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prepare Input Data", "Methods", "CompPASS", "HGScore" ], "created": "2019-02-05 21:13:59", "modified": "2026-04-21 09:25:03", "commits": 4 } ], "_score": 5.380211241711606, "_indexed": true, "_nocasepkg": "smad", "_universes": [ "bioc", "zqzneptune" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T09:49:13.000Z", "distro": "noble", "arch": "aarch64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "8ddd5e6689ebac6bdd0705c933fef3ec5ab6ad66f25e106875aab5affb770a09", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T10:20:36.000Z", "distro": "noble", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "a18375143d56ec67ee385956f55b10f17fdd44fa029181f3c651a2bd5ed40c32", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T09:48:43.000Z", "distro": "noble", "arch": "aarch64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "233f002a93f523466d4e90cc313f20199d079a62f42534330ccef828d7422e64", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T10:20:31.000Z", "distro": "noble", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "55b17c17c2d89fc0142ce1a6bac168ea346d85e9160df293ae451a3a66540e42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-30T14:30:51.000Z", "arch": "aarch64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "472115caff8ecb60de45d3e97b38b28a7d3ab9f57dbe8e7f47965045fd918966", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-30T10:09:11.000Z", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "d0b91a7004b9db54d87770829ee9b39aa2e3a90e6e35a73f19bf425af29dbddc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-30T14:31:03.000Z", "arch": "aarch64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "8fce809eb4fb75ae94bd955cc0b42c4f1632ceb300adcfbe5314f8deca34a272", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-30T10:09:05.000Z", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "1789b6c26367ae31aef6aec010a6002d1878a01cc3bd2b1163602fa7399b6c21", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-05-30T10:20:10.000Z", "arch": "emscripten", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "6d12d06643c0556f36b605b7f4473a9af96698608c835f5526b77decb9d4155f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T10:19:32.000Z", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "d1b2b8daea0ee0bc4be1a6727cd52d7c0ad81a18542a9e7c75b2f2ba079aad67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-05-30T10:19:22.000Z", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "64c69b41a91c8e49366517eb701eef2b96cb5759c334d06b9da7e8bfedea7b05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" }, { "r": "4.6.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T10:18:59.000Z", "arch": "x86_64", "commit": "8fa6b2450ea71fad11ba6bc8da2056f632198ada", "fileid": "5b0a0f7260a3434e9a333bd0690f013f561a01f2e73be3df0279747893244776", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677010216" } ] }