{ "_id": "6acdf459a14063b82c3ad77e", "Package": "pepStat", "Type": "Package", "Title": "Statistical analysis of peptide microarrays", "Version": "1.47.0", "Author": "Raphael Gottardo, Gregory C Imholte, Renan Sauteraud, Mike\nJiang", "Maintainer": "Gregory C Imholte ", "Description": "Statistical analysis of peptide microarrays", "License": "Artistic-2.0", "biocViews": "Microarray, Preprocessing", "URL": "https://github.com/RGLab/pepStat", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:21 UTC", "RemoteUrl": "https://github.com/bioc/pepStat", "RemoteRef": "HEAD", "RemoteSha": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-13 08:44:37 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "pepStat_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/c3497b6b851a1ac51d3fca75adaa5a6a5a9b3bf59d55805cddb5d26e627be93b", "_filesize": 426703, "_sha256": "c3497b6b851a1ac51d3fca75adaa5a6a5a9b3bf59d55805cddb5d26e627be93b", "_expires": "2027-01-21T09:05:27.000Z", "_created": "2026-10-13T08:44:37.000Z", "_published": "2026-10-13T09:05:29.152Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_upstream": "https://github.com/bioc/pepStat", "_commit": { "id": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379961 }, "_maintainer": { "name": "Gregory C Imholte", "email": "gimholte@uw.edu" }, "_distro": "resolute", "_jobs": [ { "job": 115209074052, "time": 211, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11799655882" }, { "job": 115209073943, "time": 310, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11799132995" }, { "job": 115209073931, "time": 337, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11799776024" }, { "job": 115209073850, "time": 173, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11800128469" }, { "job": 115209073821, "time": 204, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11800267992" }, { "job": 115207119799, "time": 298, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11799196727" }, { "job": 115209074068, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11800155005" }, { "job": 115209074110, "time": 179, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11799945163" }, { "job": 115209074106, "time": 187, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11799053289" }, { "job": 115209074016, "time": 141, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11800000173" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "limma", "role": "Imports" }, { "package": "fields", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "pepDat", "role": "Suggests" }, { "package": "Pviz", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "preprocessing" ], "_stars": 8, "_contributors": [ { "user": "gimholte", "count": 58, "uuid": 1383409 }, { "user": "srenan", "count": 51, "uuid": 1503137 }, { "user": "kevinushey", "count": 12, "uuid": 1976582 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 576, "source": "https://www.bioconductor.org/packages/stats/bioc/pepStat" }, "_mentions": 3, "_devurl": "https://github.com/rglab/pepstat", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/pepStat.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/rglab/pepstat", "_realowner": "bioc", "_cranurl": false, "_exports": [ "clade", "create_db", "featureID", "makeCalls", "makePeptideSet", "normalizeArray", "peptide", "peptide<-", "pepZscore", "pepZscore<-", "plotArrayImage", "plotArrayResiduals", "position", "ranges", "ranges<-", "restab", "shinyPepStat", "show", "slidingMean", "summarizePeptides", "width" ], "_help": [ { "page": "baseline_correct", "title": "Substract baseline intensities", "topics": [ "baseline_correct" ] }, { "page": "baselineCorrect.pSet", "title": "Substract baseline intensities", "topics": [ "baselineCorrect.pSet" ] }, { "page": "create_db", "title": "Create a peptide collection", "topics": [ "create_db" ] }, { "page": "makeCalls", "title": "Make antibody binding positivity calls", "topics": [ "makeCalls" ] }, { "page": "makePeptideSet", "title": "peptideSet constructor", "topics": [ "makePeptideSet" ] }, { "page": "normalizeArray", "title": "Normalize tiling array data using sequence information", "topics": [ "NormalizeArray", "normalizeArray" ] }, { "page": "peptideSet", "title": "peptideSet class", "topics": [ "peptideSet", "peptideSet-class" ] }, { "page": "peptideSet-methods", "title": "peptideSet methods", "topics": [ "clade", "clade,GRanges-method", "clade,peptideSet-method", "clade-methods", "end,peptideSet-method", "featureID", "featureID,peptideSet-method", "featureID-method", "peptide", "peptide,peptideSet-method", "peptide-method", "peptide<-", "peptide<-,peptideSet,character-method", "peptideSet-methods", "pepZscore", "pepZscore,GRanges-method", "pepZscore,peptideSet-method", "pepZscore-method", "pepZscore<-", "pepZscore<-,GRanges,data.frame-method", "pepZscore<-,peptideSet,data.frame-method", "position", "position,peptideSet-method", "position-method", "ranges,peptideSet-method", "ranges<-,peptideSet-method", "show,peptideSet-method", "start,peptideSet-method", "subset,peptideSet-method", "summary,peptideSet-method", "values,peptideSet-method", "width,peptideSet-method", "[,peptideSet,ANY,ANY,ANY-method" ] }, { "page": "plotArray", "title": "Plot microarray images", "topics": [ "plotArrayImage", "plotArrayResiduals" ] }, { "page": "restab", "title": "Result table", "topics": [ "restab" ] }, { "page": "shinyPepStat", "title": "Launch the pepStat Shiny Application", "topics": [ "shinyPepStat" ] }, { "page": "slidingMean", "title": "Data smoothing for peptide microarray.", "topics": [ "slidingMean" ] }, { "page": "summarizePeptides", "title": "Add information to a peptideSet and summarize peptides", "topics": [ "summarizePeptides" ] } ], "_readme": "https://github.com/bioc/pepStat/raw/HEAD/README.md", "_rundeps": [ "Biobase", "BiocGenerics", "cli", "cpp11", "data.table", "dotCall64", "farver", "fields", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lifecycle", "limma", "maps", "plyr", "R6", "RColorBrewer", "Rcpp", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "spam", "statmod", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "pepStat.Rnw", "filename": "pepStat.pdf", "title": "Full peptide microarray analysis", "engine": "knitr::knitr", "headings": [ "Introduction", "Generating a peptideSet", "Adding peptide informations", "Normalization", "Data smoothing", "Making calls", "Results", "shinyApp", "Quick analysis", "sessionInfo" ], "created": "2014-07-01 20:38:11", "modified": "2014-07-01 20:38:11", "commits": 1 } ], "_score": 5.681241237375588, "_indexed": true, "_nocasepkg": "pepstat", "_universes": [ "bioc", "rglab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-10-13T08:49:08.000Z", "distro": "resolute", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/a23652d2b0acd4c931bbe43e994c2ded6300c4976985833d37eb302c043520a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-13T08:49:34.000Z", "distro": "resolute", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/46b0dfeef2e2b00bc08957061ce87e664fd85bbdd269d13a103725751adc4170", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-13T09:03:49.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/bde1fe67ae241f795f3576f7881107526e3183c3ff6ec9dd6bacaa70e6ac1ae4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-13T09:03:36.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/c502f680b2df0f3d2ec9d12ce0b8b6116af8e1ddb8f29bc1242e66bf56478b75", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-10-13T08:47:41.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/008ef762ef3ac48c63cbc4c62520d4a0059e3b83d901f7a71c87542c89689f99", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-13T08:46:31.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/9028260806af91ad37fd5cbb6a74a1b1a79ccf3ce5882967c4187b8e3b451553", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-10-13T08:46:31.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/b91322658e974cc26156c70112d09f1384c6c97975149c101b7fca47ce07e31b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-13T08:46:20.000Z", "commit": "2688026c7ccbcfba6eeafd3e3b6227e0b13ebe4f", "fileid": "https://r2.ropensci.org/b5a00bd56d3d46864a756012d0ab3065a81134147f5eb01c7f167a6a1427a575", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38370793340" } ] }