{ "_id": "6a1f206cb401979e734203ab", "Package": "RPPASPACE", "Version": "1.0.10", "Date": "2023-10-19", "Title": "Reverse-Phase Protein Array Super Position and Concentration\nEvaluation", "Authors@R": "c(person(given = \"James M.\",\nfamily = \"Melott\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jmmelott@mdanderson.org\"\n),\nperson(given = \"Paul L.\",\nfamily = \"Roebuck\",\nrole = c(\"aut\")\n),\nperson(given = \"Kevin R.\",\nfamily = \"Coombes\",\nrole = c(\"aut\")\n),\nperson(given = \"Zhenlin\",\nfamily = \"Ju\",\nrole = c(\"aut\")\n),\nperson(given = \"Huma\",\nfamily = \"Shehwana\",\nrole = c(\"aut\")\n),\nperson(given = \"Shwetha V.\",\nfamily = \"Kumar\",\nrole = c(\"aut\")\n),\nperson(given = \"E. Shannon\",\nfamily = \"Neeley\",\nrole = c(\"aut\")\n),\nperson(given = \"Corwin\",\nfamily = \"Joy\",\nrole = c(\"aut\")\n),\nperson(given = \"Jianhua\",\nfamily = \"Hu\",\nrole = c(\"aut\")\n),\nperson(given = \"Keith A.\",\nfamily = \"Baggerly\",\nrole = c(\"aut\")\n),\nperson(given = \"Rehan\",\nfamily = \"Akbani\",\nrole = c(\"aut\"),\nemail = \"RAkbani@mdanderson.org\"\n),\nperson(given = \"Mary A.\",\nfamily = \"Rohrdanz\",\nrole = c(\"ctb\")\n),\nperson(given = \"Chris\",\nfamily = \"Wakefield\",\nrole = c(\"ctb\")\n),\nperson(given = \"Doris R.\",\nfamily = \"Siwak\",\nrole = c(\"ctb\")\n),\nperson(given = \"Yiling\",\nfamily = \"Lu\",\nrole = c(\"ctb\")\n),\nperson(given = \"Bradley M.\",\nfamily = \"Broom\",\nrole = c(\"ctb\")\n),\nperson(given = \"John N.\",\nfamily = \"Weinstein\",\nrole = c(\"ctb\")\n),\nperson(given = \"Gordon B.\",\nfamily = \"Mills\",\nrole = c(\"ctb\")\n))", "Maintainer": "James M. Melott ", "Description": "Provides tools for the analysis of reverse-phase protein\narrays (RPPAs), which are also known as 'tissue lysate arrays'\nor simply 'lysate arrays'. The package's primary purpose is to\ninput a set of quantification files representing dilution\nseries of samples and control points taken from scanned RPPA\nslides and determine a relative log concentration value for\neach valid dilution series present in each slide and provide\ngraphical visualization of the input and output data and their\nrelationships. Other optional features include generation of\nquality control scores for judging the quality of the input\ndata, spatial adjustment of sample points based on controls\nadded to the slides, and various types of normalization of\ncalculated values across a set of slides. The package was\nderived from a previous package named SuperCurve. For a\ndetailed description of data inputs and outputs, usage\ninformation, and a list of related papers describing methods\nused in the package please review the vignette\n'Guide_to_RPPASPACE'. 'RPPA SPACE: an R package for\nnormalization and quantitation of Reverse-Phase Protein Array\ndata'. Bioinformatics Nov 15;38(22):5131-5133. .", "NeedsCompilation": "no", "VignetteBuilder": "knitr, rmarkdown", "URL": "https://pubmed.ncbi.nlm.nih.gov/36205581,\nhttps://github.com/MD-Anderson-Bioinformatics/rppaspace,\nhttps://bioinformatics.mdanderson.org/public-software/rppaspace/", "License": "Artistic-2.0", "Copyright": "file inst/COPYRIGHTS", "LazyLoad": "yes", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libfftw3-dev libglpk-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libxml2-dev libx11-dev", "Repository": "https://md-anderson-bioinformatics.r-universe.dev", "Date/Publication": "2024-06-20 15:30:14 UTC", "RemoteUrl": "https://github.com/MD-Anderson-Bioinformatics/rppaspace", "RemoteRef": "HEAD", "RemoteSha": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "RemoteSubdir": "RPPASPACE", "Packaged": { "Date": "2026-05-16 07:54:43 UTC", "User": "root" }, "Author": "James M. Melott [aut, cre],\nPaul L. Roebuck [aut],\nKevin R. Coombes [aut],\nZhenlin Ju [aut],\nHuma Shehwana [aut],\nShwetha V. Kumar [aut],\nE. Shannon Neeley [aut],\nCorwin Joy [aut],\nJianhua Hu [aut],\nKeith A. Baggerly [aut],\nRehan Akbani [aut],\nMary A. Rohrdanz [ctb],\nChris Wakefield [ctb],\nDoris R. Siwak [ctb],\nYiling Lu [ctb],\nBradley M. Broom [ctb],\nJohn N. Weinstein [ctb],\nGordon B. Mills [ctb]", "MD5sum": "dc8b27c99484adb407796e1319272fef", "_user": "md-anderson-bioinformatics", "_type": "src", "_file": "RPPASPACE_1.0.10.tar.gz", "_fileid": "8442bfbc57049932b5fdc1a563f0fe4161fcc7262fa1d81aa58dbc836f07992f", "_filesize": 1807677, "_sha256": "8442bfbc57049932b5fdc1a563f0fe4161fcc7262fa1d81aa58dbc836f07992f", "_created": "2026-05-16T07:54:43.000Z", "_published": "2026-06-02T18:26:52.875Z", "_distro": "noble", "_jobs": [ { "job": 79142962352, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7031770219" }, { "job": 79142962483, "time": 196, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7031773432" }, { "job": 79142962624, "time": 113, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7031765235" }, { "job": 79142962452, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7031765204" }, { "job": 79142961720, "time": 218, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7031753968" }, { "job": 79142961394, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7366419202" }, { "job": 79142961839, "time": 146, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7031768599" }, { "job": 79142962449, "time": 99, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7031763960" }, { "job": 79142962573, "time": 110, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7031765005" } ], "_buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/MD-Anderson-Bioinformatics/rppaspace", "_commit": { "id": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "author": "James Melott ", "committer": "GitHub ", "message": "Update Guide_to_RPPASPACE.Rmd\n\nPut backticks at same indentation level so R-Universe wouldn't complain.", "time": 1718897414 }, "_maintainer": { "name": "James M. 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Melott and Keith Baggerly", "engine": "knitr::rmarkdown_notangle", "headings": [ "Purpose of the RPPASPACE R Package", "An Example to Show How It Works", "Expected Results from the Sample Code and Data", "The Biology of RPPAs", "The RPPASPACE Model", "Differences between RPPASPACE and Its Predecessor, SuperCurve", "RPPASPACE Input Data", "RPPASPACE Standard Slide Input Format", "RPPASPACE Expectations of Input Data", "Positive and Negative Controls", "Slide Layout Example", "Handling of Replicated Sample Dilution Series", "Support of Missing or Skipped Sample Series", "Randomly Ordered Slides", "The RPPASPACE Process", "Read Slide Quantification Files", "Perform Pre-Fit Quality Assurance Check", "Perform Spatial Adjustments", "Perform Curve Fitting and Calculate Relative Concentrations", "Perform Noise Quality Control Calculations", "Generate Graphical Output", "Slide Normalization", "Write Final Results", "Using RPPASPACE", "Setting Up Your R Environment", "Organizing and Formatting Of Input Data", "Creating an RPPASPACESettings Object", "Example RPPASPACE Script", "Outputs and Output Formats", "For each successfully processed slide", "One instance per slide set", "Warnings and errors output files", "Optional files based on settings object", "Error and Message Handling", "Converting Slides to Standard Slide Input Format", "Display Adapter Settings on Unix", "References" ], "created": "2020-11-09 16:55:56", "modified": "2024-06-20 15:30:14", "commits": 6 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "rppaspace", "_universes": [ "md-anderson-bioinformatics", "jmelott" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.10", "date": "2026-05-16T07:57:08.000Z", "distro": "noble", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "162d6c4d893f28596acad29e99216e90dd2fb58f9897d6646cbc1214aea8ae65", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.6.0", "os": "linux", "version": "1.0.10", "date": "2026-05-16T07:57:41.000Z", "distro": "noble", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "3d0c359447b057ef9fafac0a482381aa365a2525a77fa967eb741df94ef27300", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.5.3", "os": "mac", "version": "1.0.10", "date": "2026-05-16T07:56:36.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "75cf89b76867dd3dd520b8763c40db55edff2278c43dc39925392c08173e92e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.6.0", "os": "mac", "version": "1.0.10", "date": "2026-05-16T07:56:32.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "142f888a3b4888584f8ba00682c6a8f4cd5a8201b87b3658ba4a95b977732bea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.7.0", "os": "win", "version": "1.0.10", "date": "2026-05-16T07:56:22.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "54a12501d82260758e15ba5404041c4a2b71272a5c5ed22b8a5124b18748575e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.5.3", "os": "win", "version": "1.0.10", "date": "2026-05-16T07:56:03.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "eb62fae2dc1940ec858f98168915c7f5343c432e63a909457a90db413e16916e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.6.0", "os": "win", "version": "1.0.10", "date": "2026-05-16T07:56:20.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "9084ee22e7c3f139c7b1ada12d7f42cdcfbae967f385a32986f1bc438ec7e460", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.10", "date": "2026-06-02T18:26:29.000Z", "commit": "b2d8972ec0801df5ddda3227ec66d2dcd80877f0", "fileid": "aa8a8062396d70825c2742c55f82bcfbe5a324eb6f880c789ada4317226d7ab0", "status": "success", "buildurl": "https://github.com/r-universe/md-anderson-bioinformatics/actions/runs/25956613278" } ] }