{ "_id": "6ab23c673d719c1f8408aa75", "Package": "genArise", "Version": "1.89.0", "Title": "Microarray Analysis tool", "Author": "Ana Patricia Gomez Mayen ,\\\\ Gustavo Corral\nGuille , \\\\ Lina Riego Ruiz\n,\\\\ Gerardo Coello Coutino\n", "Acknowledgements": "Jorge Ramirez Salcedo and Microarray Unit IFC", "Maintainer": "IFC Development Team ", "Description": "genArise is an easy to use tool for dual color microarray\ndata. Its GUI-Tk based environment let any non-experienced user\nperforms a basic, but not simple, data analysis just following\na wizard. In addition it provides some tools for the developer.", "biocViews": "Microarray, TwoChannel, Preprocessing", "License": "file LICENSE", "License_restricts_use": "yes", "URL": "http://www.ifc.unam.mx/genarise", "Config/pak/sysreqs": "libx11-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:30:45 UTC", "RemoteUrl": "https://github.com/bioc/genArise", "RemoteRef": "HEAD", "RemoteSha": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-22 08:25:05 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "genArise_1.89.0.tar.gz", "_fileid": "https://r2.ropensci.org/53f908b3a01862a1065acab3a5a28760410b682f8d2149803b0d234770e74fe2", "_filesize": 1017699, "_sha256": "53f908b3a01862a1065acab3a5a28760410b682f8d2149803b0d234770e74fe2", "_expires": "2026-12-31T08:29:26.000Z", "_created": "2026-09-22T08:25:05.000Z", "_published": "2026-09-22T08:29:27.869Z", "_bioccheck": { "error": 2, "warning": 6, "note": 16 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769", "_status": "success", "_upstream": "https://github.com/bioc/genArise", "_commit": { "id": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379445 }, "_maintainer": { "name": "IFC Development Team", "email": "info-genarise@ifc.unam.mx" }, "_distro": "resolute", "_jobs": [ { "job": 106670773090, "time": 173, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "10684230478" }, { "job": 106670773250, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10683847665" }, { "job": 106670773021, "time": 219, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10683879093" }, { "job": 106670773141, "time": 84, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "10683209741" }, { "job": 106670773189, "time": 110, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "10684077081" }, { "job": 106669769381, "time": 203, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10683737284" }, { "job": 106670773116, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10684200279" }, { "job": 106670773101, "time": 75, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10683612687" }, { "job": 106670773249, "time": 75, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "10683687773" }, { "job": 106670773074, "time": 76, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10683449404" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 1.7.1", "role": "Depends" }, { "package": "locfit", "role": "Depends" }, { "package": "tkrplot", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tcltk", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "xtable", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.89.0", "bioc": "3.24" }, { "branch": "release", "version": "1.88.0", "bioc": "3.23" } ], "_topics": [ "microarray", "twochannel", "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 532, "source": "https://www.bioconductor.org/packages/stats/bioc/genArise" }, "_mentions": 16, "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/genArise.html", "extra/manual.pdf", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "a.arise", "alter.unique", "analysis.window", "annotations", "back.gui", "bg.correct", "create.project", "cys.plot", "filter.spot", "genArise", "genArise.init", "genMerge", "get.values", "get.Zscore", "global.norm", "graphic.choose", "grid.norm", "help", "i.arise", "imageLimma", "m.arise", "ma.plot", "make.swap", "meanUnique", "note", "old.project", "post.analysis", "principal", "projects.select", "r.arise", "read.dataset", "read.spot", "reset.history", "ri.plot", "set.grid.properties", "set.history.project", "set.path.project", "set.project.properties", "single.norm", "spotUnique", "swap.select", "trim", "write.dataSet", "write.spot", "write.zscore", "Zscore", "Zscore.plot", "Zscore.points" ], "_datasets": [ { "name": "Simon", "title": "Dataset: Little fragment of a microarray from IFC UNAM", "object": "Simon", "file": "Simon.rda", "class": [ "Spot" ], "fields": [], "table": true, "tojson": false }, { "name": "WT.dataset", "title": "Microarray from the IFC", "object": "WT.dataset", "file": "WT.dataset.rda", "class": [ "DataSet" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "a.arise", "title": "A Arise", "topics": [ "a.arise" ] }, { "page": "alter.unique", "title": "Remove Duplicates", "topics": [ "alter.unique" ] }, { "page": "analysis.window", "title": "Analysis.window", "topics": [ "analysis.window" ] }, { "page": "annotations", "title": "Gene Annotations", "topics": [ "annotations" ] }, { "page": "back.gui", "title": "Return to the last window", "topics": [ "back.gui" ] }, { "page": "bg.correct", "title": "Background Correction", "topics": [ "bg.correct" ] }, { "page": "classes", "title": "Classes Defined by this Package", "topics": [ "classes" ] }, { "page": "create.project", "title": "Create directorie for the project and its results and graphics", "topics": [ "create.project" ] }, { "page": "cys.plot", "title": "Data Visualization: log2(Cy3) vs log2(Cy5)", "topics": [ "cys.plot" ] }, { "page": "DataSet-class", "title": "DataSet - class", "topics": [ "DataSet-class" ] }, { "page": "filter.spot", "title": "Intensity-based filtering of array elements", "topics": [ "filter.spot" ] }, { "page": "genArise", "title": "GUI: Graphical User Interface", "topics": [ "genArise" ] }, { "page": "genArise.init", "title": "genArise.init", "topics": [ "genArise.init" ] }, { "page": "genMerge", "title": "genMerge: Post-Genomic Analysis", "topics": [ "genMerge" ] }, { "page": "get.values", "title": "Auxiliar function for post-analysis", "topics": [ "get.values" ] }, { "page": "get.Zscore", "title": "Swap from Files", "topics": [ "get.Zscore" ] }, { "page": "global.norm", "title": "Global Normalization of Spot", "topics": [ "global.norm" ] }, { "page": "graphic.choose", "title": "Graphic choose", "topics": [ "graphic.choose" ] }, { "page": "grid.norm", "title": "Normalization by grid of Spot", "topics": [ "grid.norm" ] }, { "page": "help", "title": "Help of genArise", "topics": [ "help" ] }, { "page": "i.arise", "title": "I Arise", "topics": [ "i.arise" ] }, { "page": "imageLimma", "title": "Image Plot of Microarray", "topics": [ "imageLimma" ] }, { "page": "m.arise", "title": "M Arise", "topics": [ "m.arise" ] }, { "page": "ma.plot", "title": "Data Visualization: M vs. A plot", "topics": [ "ma.plot" ] }, { "page": "make.swap", "title": "Swap analysis", "topics": [ "make.swap" ] }, { "page": "meanUnique", "title": "Remove Duplicates", "topics": [ "meanUnique" ] }, { "page": "note", "title": "note", "topics": [ "note" ] }, { "page": "old.project", "title": "Open previous project", "topics": [ "old.project" ] }, { "page": "post.analysis", "title": "Set-combinatorial analysis", "topics": [ "post.analysis" ] }, { "page": "principal", "title": "Principal window of genAriseGUI", "topics": [ "principal" ] }, { "page": "projects.select", "title": "File selector", "topics": [ "projects.select" ] }, { "page": "r.arise", "title": "Get R value", "topics": [ "r.arise" ] }, { "page": "read.dataset", "title": "Read Dataset from File", "topics": [ "read.dataset" ] }, { "page": "read.spot", "title": "Read Spot from File", "topics": [ "read.spot" ] }, { "page": "reset.history", "title": "Reset the prj history file", "topics": [ "reset.history" ] }, { "page": "ri.plot", "title": "Data Visualization: R vs I", "topics": [ "ri.plot" ] }, { "page": "set.grid.properties", "title": "set.grid.properties", "topics": [ "set.grid.properties" ] }, { "page": "set.history.project", "title": "Save the history of a project", "topics": [ "set.history.project" ] }, { "page": "set.path.project", "title": "set.path.project", "topics": [ "set.path.project" ] }, { "page": "set.project.properties", "title": "set.project.properties", "topics": [ "set.project.properties" ] }, { "page": "Simon", "title": "Dataset: Little fragment of a microarray from IFC UNAM", "topics": [ "Simon" ] }, { "page": "single.norm", "title": "Swap from Files", "topics": [ "single.norm" ] }, { "page": "Spot-class", "title": "Spot - class", "topics": [ "Spot-class" ] }, { "page": "spotUnique", "title": "Replicate filtering", "topics": [ "spotUnique" ] }, { "page": "swap.select", "title": "Dye swap files selector", "topics": [ "swap.select" ] }, { "page": "trim", "title": "Trim", "topics": [ "trim" ] }, { "page": "write.dataSet", "title": "Write dataSet", "topics": [ "write.dataSet" ] }, { "page": "write.spot", "title": "Write Spot", "topics": [ "write.spot" ] }, { "page": "write.zscore", "title": "Write Z-score data", "topics": [ "write.zscore" ] }, { "page": "WT.dataset", "title": "Microarray from the IFC", "topics": [ "WT.dataset" ] }, { "page": "Zscore", "title": "Z-scores for identifying differential expression", "topics": [ "Zscore" ] }, { "page": "Zscore.plot", "title": "Z-score Data Visualization: R vs I or M vs A", "topics": [ "Zscore.plot" ] }, { "page": "Zscore.points", "title": "Z-score Window", "topics": [ "Zscore.points" ] } ], "_rundeps": [ "lattice", "locfit", "tkrplot", "xtable" ], "_vignettes": [ { "source": "genArise.Rnw", "filename": "genArise.pdf", "title": "genAriseGUI Vignette", "engine": "utils::Sweave", "headings": [ "Introduction", "The genArise Package's Functions", "The genArise GUI" ], "created": "2013-11-01 19:52:30", "modified": "2013-11-01 19:52:30", "commits": 1 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "genarise", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.89.0", "date": "2026-09-22T08:28:24.000Z", "distro": "resolute", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/a7d9c2b84c04c6ffb78c13063ab3482756194de1336c4f685785dd7ba626130f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.6.1", "os": "linux", "version": "1.89.0", "date": "2026-09-22T08:28:44.000Z", "distro": "resolute", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/afb7dadffb5a551feafe8c44d308a97f31512cc01488469135e881f32fc85aa3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.5.3", "os": "mac", "version": "1.89.0", "date": "2026-09-22T08:26:38.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/641929e93ace39eb693b330c3b38c4d93cb315b630b11b997bb8d8512bf5ad23", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.6.1", "os": "mac", "version": "1.89.0", "date": "2026-09-22T08:26:57.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/00b4e9f93b3d20358983ac0173b9800dc520ad00086fd10208e4ffc72c28a00c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.6.0", "os": "wasm", "version": "1.89.0", "date": "2026-09-22T08:27:31.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/dedb6cd038ea894cf4e23f067dd81b20b2d47b5661753d863399bc82b4d70a61", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.7.0", "os": "win", "version": "1.89.0", "date": "2026-09-22T08:26:13.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/37cd4ab793fdf88c907270c336c35e734b447a3fd3d52b1d78d30e8222b3d8c2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.5.3", "os": "win", "version": "1.89.0", "date": "2026-09-22T08:26:19.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/7067bdccd47bce205bd08882491bd129a85f9525df8dadb77263ded82bcc065b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" }, { "r": "4.6.1", "os": "win", "version": "1.89.0", "date": "2026-09-22T08:26:12.000Z", "commit": "fcaf847e16d8feb1d3a79083e205a239a45a8908", "fileid": "https://r2.ropensci.org/1b541998c9103f7ea3dfb6293f0ad3b272133c3e79df06dc2d4707101b1405d4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35704370769" } ] }