{ "_id": "6a1ac1161d7bb097a09d77ba", "Package": "NuPoP", "Type": "Package", "Title": "An R package for nucleosome positioning prediction", "Version": "2.21.0", "Date": "2020-11-21", "Author": "Ji-Ping Wang ; Liqun Xi\n; Oscar Zarate ", "Maintainer": "Ji-Ping Wang", "Description": "NuPoP is an R package for Nucleosome Positioning\nPrediction.This package is built upon a duration hidden Markov\nmodel proposed in Xi et al, 2010; Wang et al, 2008. The core of\nthe package was written in Fotran. In addition to the R\npackage, a stand-alone Fortran software tool is also available\nat https://github.com/jipingw. The Fortran codes have complete\nfunctonality as the R package. Note: NuPoP has two separate\nfunctions for prediction of nucleosome positioning, one for\nMNase-map trained models and the other for chemical map-trained\nmodels. The latter was implemented for four species including\nyeast, S.pombe, mouse and human, trained based on our recent\npublications. We noticed there is another package nuCpos by\nanother group for prediction of nucleosome positioning trained\nwith chemicals. A report to compare recent versions of NuPoP\nwith nuCpos can be found at\nhttps://github.com/jiping/NuPoP_doc. Some more information can\nbe found and will be posted at\nhttps://github.com/jipingw/NuPoP.", "License": "GPL-2", "biocViews": "Genetics,Visualization,Classification,NucleosomePositioning,\nHiddenMarkovModel", "NeedsCompilation": "yes", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:48 UTC", "RemoteUrl": "https://github.com/bioc/NuPoP", "RemoteRef": "HEAD", "RemoteSha": "260a6303040b2e88c83445f4ee6aa560ec81d364", "Packaged": { "Date": "2026-05-30 07:21:50 UTC", "User": "root" }, "MD5sum": "4a053d6c5bb3e79c8837507758ee6f8d", "_user": "bioc", "_type": "src", "_file": "NuPoP_2.21.0.tar.gz", "_fileid": "1d93d86c45da38741cdc4bee7d97b68f6462018e8e219674609027176d599592", "_filesize": 6359818, "_sha256": "1d93d86c45da38741cdc4bee7d97b68f6462018e8e219674609027176d599592", "_created": "2026-05-30T07:21:50.000Z", "_published": "2026-05-30T10:51:02.184Z", "_jobs": [ { "job": 78633174117, "time": 134, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306440957" }, { "job": 78633174136, "time": 171, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306444644" }, { "job": 78633174148, "time": 147, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306442161" }, { "job": 78633174161, "time": 119, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306439349" }, { "job": 78633174146, "time": 152, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306442634" }, { "job": 78633174152, "time": 97, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307551523" }, { "job": 78633174157, "time": 200, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306542589" }, { "job": 78633174149, "time": 103, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307553762" }, { "job": 78633174153, "time": 199, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306540619" }, { "job": 78633016894, "time": 176, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306426470" }, { "job": 78633174128, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306437004" }, { "job": 78633174137, "time": 100, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7306437441" }, { "job": 78633174135, "time": 93, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7306436590" }, { "job": 78633174145, "time": 140, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7306441473" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/NuPoP", "_commit": { "id": "260a6303040b2e88c83445f4ee6aa560ec81d364", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379688 }, "_maintainer": { "name": "Ji-Ping Wang", "email": "jzwang@northwestern.edu", "login": "jipingw", "description": "Professor in Statistics and Data Science, Adjunct Professor of Molecular BioSciences. My research interest is in interface of statistics and bi-medical sciences", "uuid": 45120092 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.21.0", "bioc": "3.24" }, { "branch": "release", "version": "2.20.0", "bioc": "3.23" } ], "_topics": [ "genetics", "visualization", "classification", "nucleosomepositioning", "hiddenmarkovmodel", "fortran" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 450, "source": "https://www.bioconductor.org/packages/stats/bioc/NuPoP" }, "_mentions": 18, "_searchresults": 17, "_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/NuPoP.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jipingw/nupop", "_realowner": "bioc", "_cranurl": false, "_exports": [ "plotNuPoP", "predNuPoP", "predNuPoP_chem", "readNuPoP" ], "_help": [ { "page": "NuPoP-package", "title": "An R package for nucleosome positioning prediction", "topics": [ "NuPoP-package", "NuPoP" ] }, { "page": "plotNuPoP", "title": "R function for plotting the predicted nucleosome positioning map and nucleosome occupancy map", "topics": [ "plotNuPoP" ] }, { "page": "predNuPoP", "title": "R function for nucleosome positioning prediction, occupancy score and nucleosome binding affinity score calculation", "topics": [ "predNuPoP" ] }, { "page": "predNuPoP_chem", "title": "R function for nucleosome positioning prediction, occupancy score and nucleosome binding affinity score calculation using chemical map profile", "topics": [ "predNuPoP_chem" ] }, { "page": "readNuPoP", "title": "R function for plotting the predicted nucleosome positioning map and nucleosome occupancy map", "topics": [ "readNuPoP" ] } ], "_readme": "https://github.com/bioc/NuPoP/raw/HEAD/README.md", "_rundeps": [], "_sysdeps": [ { "shlib": "libgfortran", "package": "libgfortran5", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "fortran", "homepage": "http://gcc.gnu.org/", "description": "Runtime library for GNU Fortran applications" } ], "_vignettes": [ { "source": "NuPoP.Rmd", "filename": "NuPoP.html", "title": "NuPoP: Nucleosomes Positioning Prediction", "author": "Ji-Ping Wang, Liqun Xi and Oscar Zarate", "engine": "knitr::rmarkdown", "headings": [ "NuPoP versions hightlights", "About NuPoP", "NuPoP functions", "Session info" ], "created": "2020-11-21 13:05:02", "modified": "2022-08-09 11:16:50", "commits": 3 } ], "_score": 5.230448921378274, "_indexed": true, "_nocasepkg": "nupop", "_universes": [ "bioc", "jipingw" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.21.0", "date": "2026-05-30T07:24:42.000Z", "distro": "noble", "arch": "aarch64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "e1dda633e2cc6f10e36247a903da9f1ff841653b708d339786e3367e7468e7c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.7.0", "os": "linux", "version": "2.21.0", "date": "2026-05-30T07:24:17.000Z", "distro": "noble", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "6af92e2bff932785d23dca2e5a9317ef9f42c13405f3ff8efd39aec3a9314c25", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "linux", "version": "2.21.0", "date": "2026-05-30T07:23:56.000Z", "distro": "noble", "arch": "aarch64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "2f3f2376e331ecaa058abfb1010423662acd6c5c50007cc9b9a8e7affd1da36b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "linux", "version": "2.21.0", "date": "2026-05-30T07:24:22.000Z", "distro": "noble", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "1abe229d574a17ab8bfdbb0f80512669d1fb4c8955ebbd4a198b858a1d87cf32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.5.3", "os": "mac", "version": "2.21.0", "date": "2026-05-30T10:35:01.000Z", "arch": "aarch64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "8aed49f223e76e7503dc7c17e3523f50039b240aee584a12066484d6efe4e56b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.5.3", "os": "mac", "version": "2.21.0", "date": "2026-05-30T07:39:12.000Z", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "21fe378cd4086d64f58b16d26c27ad5277ca74272d23c64d8c090949d7fbf691", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "mac", "version": "2.21.0", "date": "2026-05-30T10:35:22.000Z", "arch": "aarch64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "8f65d70f1b756b98ea52676c7372e46c9e7775d656f3897a1712de949f3bbbe2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "mac", "version": "2.21.0", "date": "2026-05-30T07:38:49.000Z", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "dccf4cb7382a04ebf03e8f6c68ff15c2c06f60d8bf40ff3470cecb707a4c3ced", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "wasm", "version": "2.21.0", "date": "2026-05-30T07:23:45.000Z", "arch": "emscripten", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "9f1131f2e8ab1866047bb2149719fcfe05a0ace3c124e73fa9d6d64a94ed0a33", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.7.0", "os": "win", "version": "2.21.0", "date": "2026-05-30T07:23:18.000Z", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "724a685febaad4c4786ea760778855d3a863dde02929ccf8b5f6efeb6a78d2fe", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.5.3", "os": "win", "version": "2.21.0", "date": "2026-05-30T07:23:15.000Z", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "31be9ec97eddaa19c412918925efae48c23bc781f4ee2357f1b713890ab294d9", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" }, { "r": "4.6.0", "os": "win", "version": "2.21.0", "date": "2026-05-30T07:23:54.000Z", "arch": "x86_64", "commit": "260a6303040b2e88c83445f4ee6aa560ec81d364", "fileid": "3c65a65476d3abc026d7c317ea524e8a333893bc4830fba424d022f7a335c4e4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677887501" } ] }