{ "_id": "6ad09805cf31981cbb6ef809", "Package": "PEIMAN2", "Title": "Post-Translational Modification Enrichment, Integration, and\nMatching Analysis", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Mohieddin\", \"Jafari\", role = c(\"aut\"),email = \"mohieddin.jafari@helsinki.fi\"),\nperson(\"Payman\", \"Nickchi\", role = c(\"aut\",\"cre\"),email = \"payman.nickchi@gmail.com\")\n)", "Description": "Functions and mined database from 'UniProt' focusing on\npost-translational modifications to do single enrichment\nanalysis (SEA) and protein set enrichment analysis (PSEA).\nPayman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc\nBaumann, Amir Ata Saei, Mohieddin Jafari (2025)\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "LazyData": "true", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 08:26:14 UTC", "User": "root" }, "Author": "Mohieddin Jafari [aut], Payman Nickchi [aut, cre]", "Maintainer": "Payman Nickchi ", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://pnickchi.r-universe.dev", "Date/Publication": "2026-06-17 19:59:21 UTC", "RemoteUrl": "https://github.com/pnickchi/peiman2", "RemoteRef": "HEAD", "RemoteSha": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "_user": "pnickchi", "_type": "src", "_file": "PEIMAN2_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/09547ba842b2d7fc9a2dbcc68a281b15ff7f49362a29754952ebf405ff44aaca", "_filesize": 8149532, "_sha256": "09547ba842b2d7fc9a2dbcc68a281b15ff7f49362a29754952ebf405ff44aaca", "_expires": "2027-01-23T09:08:19.000Z", "_created": "2026-10-15T08:26:14.000Z", "_published": "2026-10-15T09:08:21.459Z", "_buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116324519251, "time": 156, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11958771315" }, { "job": 116324519486, "time": 213, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11958039569" }, { "job": 116324519523, "time": 124, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11960705500" }, { "job": 116324519693, "time": 168, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11960550705" }, { "job": 116322253776, "time": 338, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11958281628" }, { "job": 116324519386, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11958820971" }, { "job": 116324519265, "time": 128, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11957878705" }, { "job": 116324519267, "time": 90, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11958696324" }, { "job": 116324519475, "time": 127, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11958850775" } ], "_upstream": "https://github.com/pnickchi/peiman2", "_commit": { "id": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "author": "Payman Nickchi ", "committer": "Payman Nickchi ", "message": "Update GitHub Actions checkout to v5\n", "time": 1781726361 }, "_maintainer": { "name": "Payman Nickchi", "email": "payman.nickchi@gmail.com", "login": "pnickchi", "description": "", "uuid": 22579712 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "forcats", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "pnickchi", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-08", "n": 3 }, { "week": "2026-25", "n": 11 } ], "_tags": [ { "name": "v1.1.0", "date": "2026-06-17" } ], "_stars": 2, "_contributors": [ { "user": "pnickchi", "count": 123, "uuid": 22579712 }, { "user": "jafarilab", "count": 2, "uuid": 28731506 } ], "_userbio": { "uuid": 22579712, "type": "user", "name": "Payman Nickchi", "followers": 1 }, "_downloads": { "count": 409, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PEIMAN2" }, "_devurl": "https://github.com/pnickchi/peiman2", "_searchresults": 9, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/PEIMAN2.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/pnickchi/peiman2", "_realowner": "pnickchi", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2022-11-21" }, { "version": "1.0.0", "date": "2025-04-08" }, { "version": "1.0.1", "date": "2025-05-31" }, { "version": "1.0.2", "date": "2026-02-16" }, { "version": "1.1.0", "date": "2026-06-17" } ], "_exports": [ "getTaxonomyName", "plotEnrichment", "plotPSEA", "plotRunningScore", "psea2mass", "runEnrichment", "runPSEA", "sea2mass", "update_peiman_database" ], "_datasets": [ { "name": "exmplData1", "title": "Example dataset1", "object": "exmplData1", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "exmplData2", "title": "Example dataset 2", "object": "exmplData2", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "UniProtAC", "Score" ], "rows": 209, "table": true, "tojson": true }, { "name": "mod_ont", "title": "Database of protein modifications", "object": "mod_ont", "class": [ "data.frame" ], "fields": [ "id", "name", "def" ], "rows": 2102, "table": true, "tojson": true }, { "name": "ptmlist", "title": "Controlled vocabulary for post-translational modifications (PTM) terms", "object": "ptmlist", "class": [ "data.frame" ], "fields": [ "ID", "AC", "KW", "FT", "DR" ], "rows": 715, "table": true, "tojson": true } ], "_help": [ { "page": "exmplData1", "title": "Example dataset1", "topics": [ "exmplData1" ] }, { "page": "exmplData2", "title": "Example dataset 2", "topics": [ "exmplData2" ] }, { "page": "getTaxonomyName", "title": "Return the exact taxonomy name for list of protein", "topics": [ "getTaxonomyName" ] }, { "page": "mod_ont", "title": "Database of protein modifications", "topics": [ "mod_ont" ] }, { "page": "plotEnrichment", "title": "Plot and match singular enrichment results", "topics": [ "plotEnrichment" ] }, { "page": "plotPSEA", "title": "Plot the results of protein set enrichment analysis (PSEA)", "topics": [ "plotPSEA" ] }, { "page": "plotRunningScore", "title": "Plot running score plot for the results of psea", "topics": [ "plotRunningScore" ] }, { "page": "psea2mass", "title": "Translate PSEA results for Mass Spectrometry searching tools", "topics": [ "psea2mass" ] }, { "page": "ptmlist", "title": "Controlled vocabulary for post-translational modifications (PTM) terms", "topics": [ "ptmlist" ] }, { "page": "runEnrichment", "title": "Run singular enrichment analysis (SEA) for a given list of protein", "topics": [ "runEnrichment" ] }, { "page": "runPSEA", "title": "Run Protein Set Enrichment Analysis (PSEA)", "topics": [ "runPSEA" ] }, { "page": "sea2mass", "title": "Translate SEA results for Mass Spectrometry searching tools", "topics": [ "sea2mass" ] }, { "page": "update_peiman_database", "title": "Download and cache PEIMAN2 external data files", "topics": [ "update_peiman_database" ] } ], "_readme": "https://github.com/pnickchi/peiman2/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "forcats", "generics", "ggplot2", "glue", "gtable", "isoband", "jsonlite", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "PEIMAN2-vignette.Rmd", "filename": "PEIMAN2-vignette.html", "title": "PEIMAN2-vignette", "author": "Payman Nickchi, Mohieddin Jafari", "engine": "knitr::rmarkdown", "headings": [ "1 Introduction", "2 Example data", "3 Singular Enrichment analysis (SEA)", "3.1 Enrichment", "3.2 Plotting SEA results", "4 Protein set enrichment analysis (PSEA)", "4.1 PSEA", "4.2 Plotting", "5. Translate PEIMAN results for Mass spectrometry searching tools", "References" ], "created": "2022-04-20 04:03:04", "modified": "2025-03-05 00:59:49", "commits": 12 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "peiman2", "_universes": [ "pnickchi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-10-15T08:28:36.000Z", "distro": "resolute", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/c1a38fb192c5790a10f03a0a4f13a982b242d2a1f4af9437273641f978057c70", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-10-15T08:29:21.000Z", "distro": "resolute", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/f9a0d4df4c04934bc54bfc741a32b447a7cf9f856ea247365354d689d6ad27da", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-10-15T09:07:10.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/df17af436fdfd8909aeb3dba9b9d3f4f1236653c2f3b3523aac690be1fdb4bff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-10-15T09:06:50.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/bbe911ca52d6d1535762095b016c4112be3ebec3da438c3635cbd9d3ad9fe974", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-10-15T08:28:23.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/de13766ab831106060cebca3f1a98e4c473300a7053fcfacc5e4325dd41f62d2", "status": "success", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-10-15T08:27:50.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/36d815873206bd486dbc4f80b917566f9d035765f3cc91a6648f4ae89c5cac7a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-10-15T08:27:37.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/fdefff5debcc8841cf8e2459fd501810b52ffde36730eeabd0d632b01d4e8560", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-10-15T08:27:53.000Z", "commit": "04de2f117ab43a03ba85fe7175a0e7abaab6568a", "fileid": "https://r2.ropensci.org/f04d663830a7bf3b5bfd950268a80f212df00d648002d3e394edd72ce9359ce1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pnickchi/actions/runs/38705000534" } ] }