{ "_id": "6ad868b4d556c3a3418a825c", "Package": "pepXMLTab", "Type": "Package", "Title": "Parsing pepXML files and filter based on peptide FDR.", "Version": "1.47.0", "Date": "2015-09-20", "Author": "Xiaojing Wang", "Maintainer": "Xiaojing Wang ", "Description": "Parsing pepXML files based one XML package. The package\ntries to handle pepXML files generated from different\nsoftwares. The output will be a peptide-spectrum-matching\ntabular file. The package also provide function to filter the\nPSMs based on FDR.", "License": "Artistic-2.0", "biocViews": "ImmunoOncology, Proteomics, MassSpectrometry", "Config/pak/sysreqs": "libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:14 UTC", "RemoteUrl": "https://github.com/bioc/pepXMLTab", "RemoteRef": "HEAD", "RemoteSha": "a49de2215c3801a932d52aae976835b471946ae0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-21 06:58:18 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "pepXMLTab_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/4e448fa347bb41907dc338ab9776fd36d749be70d85d92d0fa53ea05356957e0", "_filesize": 277648, "_sha256": "4e448fa347bb41907dc338ab9776fd36d749be70d85d92d0fa53ea05356957e0", "_expires": "2027-01-29T07:24:35.000Z", "_created": "2026-10-21T06:58:18.000Z", "_published": "2026-10-21T07:24:36.879Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 2, "note": 4 }, "_upstream": "https://github.com/bioc/pepXMLTab", "_commit": { "id": "a49de2215c3801a932d52aae976835b471946ae0", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380014 }, "_maintainer": { "name": "Xiaojing Wang", "email": "xiaojing.wang@vanderbilt.edu" }, "_distro": "resolute", "_jobs": [ { "job": 119084881247, "time": 124, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12327305912" }, { "job": 119084881194, "time": 232, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12326254990" }, { "job": 119084881129, "time": 188, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12326543090" }, { "job": 119084881180, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12328565035" }, { "job": 119084881055, "time": 118, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12327711624" }, { "job": 119084030158, "time": 144, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12326861450" }, { "job": 119084881076, "time": 88, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12326667436" }, { "job": 119084881522, "time": 73, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12326926966" }, { "job": 119084881265, "time": 53, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12326632403" }, { "job": 119084881464, "time": 56, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12327445063" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.1", "role": "Depends" }, { "package": "XML", "version": ">= 3.98-1.1", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "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": [ "immunooncology", "proteomics", "massspectrometry" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 500, "source": "https://www.bioconductor.org/packages/stats/bioc/pepXMLTab" }, "_mentions": 2, "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/pepXMLTab.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "pepXML2tab", "PSMfilter" ], "_help": [ { "page": "pepXML2tab", "title": "Generate a data frame objects from a pepXML file.", "topics": [ "pepXML2tab" ] }, { "page": "PSMfilter", "title": "Filter the peptide indentification.", "topics": [ "PSMfilter" ] } ], "_rundeps": [ "XML" ], "_vignettes": [ { "source": "pepXMLTab.Rnw", "filename": "pepXMLTab.pdf", "title": "Introduction to pepXMLTab", "engine": "utils::Sweave", "headings": [ "Introduction", "Convert pepXML to a tabular format", "PSMs Filtering", "Session Information" ], "created": "2014-10-14 02:29:51", "modified": "2014-10-14 02:29:51", "commits": 1 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "pepxmltab", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-10-21T07:02:17.000Z", "distro": "resolute", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/b224cfc404f6a65f478955cbdd69659e59a283f4f3ae7d9677b437f3d251e55d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-21T07:01:34.000Z", "distro": "resolute", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/5a43ec3ed3e8a5a1b9b197bed3d7c8ad2c372982e8b449b070b874fac4e2bc03", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-21T07:24:07.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/8a236b2b42a9389f30bfeb356424e9d6f37fee52a702ee3fa73a0d0ca447beaf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-21T07:16:44.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/a0e54126bc787e67aa451536b35bfcd94c5d5e3dc5cf2bb46e789752c0d7960d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-10-21T07:00:03.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/9c1f9ff4261bd34c1aabe6d92567c3fdaeca79da0a972335357ec4c579acbdc9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-21T06:59:34.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/d9f69e0a734a2f21300f05a366adcca3aa2240f8d4438688150394a41f9f50b5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-10-21T06:59:14.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/2ab13ce5e4175308b75e0e77506435a8677ca52d9a144c2ab8258a25ba2852cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-21T06:59:17.000Z", "commit": "a49de2215c3801a932d52aae976835b471946ae0", "fileid": "https://r2.ropensci.org/653703b4d1ae331e347c2dea4a304388c9dbcca98b3d2b0ca94419fc3db7b073", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39558514504" } ] }