{
  "_id": "6a1aeaea1d7bb097a09f399b",
  "Package": "SmartPhos",
  "Type": "Package",
  "Title": "A phosphoproteomics data analysis package with an interactive\nShinyApp",
  "Version": "1.3.0",
  "Authors@R": "c(person(\"Shubham\", \"Agrawal\", role = c(\"aut\", \"cre\"), \nemail = \"shubhamagrawal2706@gmail.com\",\ncomment = c(ORCID = \"0009-0005-2630-9342\")),\nperson(\"Junyan\", \"Lu\", role = c(\"aut\"),\nemail = \"jylu1118@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9211-0746\")))",
  "Description": "To facilitate and streamline phosphoproteomics data\nanalysis, we developed SmartPhos, an R package for the\npre-processing, quality control, and exploratory analysis of\nphosphoproteomics data generated by MaxQuant and Spectronaut.\nThe package can be used either through the R command line or\nthrough an interactive ShinyApp called SmartPhos Explorer. The\npackage contains methods such as normalization and\nnormalization correction, transformation, imputation, batch\neffect correction, PCA, heatmap, differential expression,\ntime-series clustering, gene set enrichment analysis, and\nkinase activity inference.",
  "License": "GPL-3",
  "biocViews": "Visualization, ShinyApps, GUI, QualityControl, Proteomics,\nDifferentialExpression, Normalization, Preprocessing,\nGeneSetEnrichment, Clustering, GeneExpression,\nMassSpectrometry, BatchEffect",
  "BugReports": "https://github.com/Bioconductor/SmartPhos/issues",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "URL": "https://lu-group-ukhd.github.io/SmartPhos/",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:46 UTC",
  "RemoteUrl": "https://github.com/bioc/SmartPhos",
  "RemoteRef": "HEAD",
  "RemoteSha": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:38:58 UTC",
    "User": "root"
  },
  "Author": "Shubham Agrawal [aut, cre] (ORCID:\n<https://orcid.org/0009-0005-2630-9342>),\nJunyan Lu [aut] (ORCID: <https://orcid.org/0000-0002-9211-0746>)",
  "Maintainer": "Shubham Agrawal <shubhamagrawal2706@gmail.com>",
  "MD5sum": "4bb822d6cb654fe28a3b2b3b49f11f56",
  "_user": "bioc",
  "_type": "src",
  "_file": "SmartPhos_1.3.0.tar.gz",
  "_fileid": "000f316dd2c159ca40de97f2842fd33f17db8dd5c3071b034a9bf7f3a0f8ee27",
  "_filesize": 20744145,
  "_sha256": "000f316dd2c159ca40de97f2842fd33f17db8dd5c3071b034a9bf7f3a0f8ee27",
  "_created": "2026-05-30T09:38:58.000Z",
  "_published": "2026-05-30T13:49:30.357Z",
  "_jobs": [
    {
      "job": 78640223181,
      "time": 242,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307365180"
    },
    {
      "job": 78640223207,
      "time": 441,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307383990"
    },
    {
      "job": 78640223169,
      "time": 542,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307393039"
    },
    {
      "job": 78640223184,
      "time": 235,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308630366"
    },
    {
      "job": 78640223167,
      "time": 318,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308637610"
    },
    {
      "job": 78639497859,
      "time": 377,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307243328"
    },
    {
      "job": 78640223168,
      "time": 211,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307362660"
    },
    {
      "job": 78640223194,
      "time": 392,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307380982"
    },
    {
      "job": 78640223201,
      "time": 324,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307374731"
    },
    {
      "job": 78640223192,
      "time": 359,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307377902"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SmartPhos",
  "_commit": {
    "id": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381546
  },
  "_maintainer": {
    "name": "Shubham Agrawal",
    "email": "shubhamagrawal2706@gmail.com",
    "login": "shubh2565",
    "description": "",
    "uuid": 29269168
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinythemes",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "shinyBS",
      "role": "Imports"
    },
    {
      "package": "shinyWidgets",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "ggbeeswarm",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "MsCoreUtils",
      "role": "Imports"
    },
    {
      "package": "imputeLCMD",
      "role": "Imports"
    },
    {
      "package": "missForest",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "proDA",
      "role": "Imports"
    },
    {
      "package": "decoupleR",
      "role": "Imports"
    },
    {
      "package": "piano",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "vsn",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "PhosR",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 8
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.3.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.2.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "visualization",
    "shinyapps",
    "gui",
    "qualitycontrol",
    "proteomics",
    "differentialexpression",
    "normalization",
    "preprocessing",
    "genesetenrichment",
    "clustering",
    "geneexpression",
    "massspectrometry",
    "batcheffect"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 82,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SmartPhos"
  },
  "_pkgdown": "https://lu-group-ukhd.github.io/SmartPhos/",
  "_searchresults": 4,
  "_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/readme.html",
    "extra/readme.md",
    "extra/SmartPhos.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addZeroTime",
    "calcKinaseScore",
    "checkRatioMat",
    "clusterEnrich",
    "clusterTS",
    "enrichDifferential",
    "getDecouplerNetwork",
    "getRatioMatrix",
    "intensityBoxPlot",
    "makeSmartPhosDirectory",
    "medianNorm",
    "mscale",
    "normByFullProteome",
    "performCombinedNormalization",
    "performDifferentialExp",
    "plotAdjustmentResults",
    "plotHeatmap",
    "plotIntensity",
    "plotKinaseDE",
    "plotKinaseTimeSeries",
    "plotLogRatio",
    "plotMissing",
    "plotPCA",
    "plotTimeSeries",
    "plotVolcano",
    "preprocessPhos",
    "preprocessProteome",
    "readExperiment",
    "readExperimentDIA",
    "readPhosphoExperiment",
    "readPhosphoExperimentDIA",
    "readProteomeExperiment",
    "readProteomeExperimentDIA",
    "runFisher",
    "runGSEAforPhospho",
    "runPhosphoAdjustment",
    "runSmartPhos"
  ],
  "_datasets": [
    {
      "name": "dda_example",
      "title": "dda_example",
      "object": "dda_example",
      "file": "dda_example.rda",
      "class": [
        "MultiAssayExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dia_example",
      "title": "dia_example",
      "object": "dia_example",
      "file": "dia_example.rda",
      "class": [
        "MultiAssayExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Homo_sapien_kinase_substrate_network",
      "title": "Homo_sapien_kinase_substrate_network",
      "object": "Homo_sapien_kinase_substrate_network",
      "file": "Homo_sapien_kinase_substrate_network.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "source",
        "mor",
        "target",
        "likelihood"
      ],
      "rows": 32103,
      "table": true,
      "tojson": true
    },
    {
      "name": "Mus_musculus_kinase_substrate_network",
      "title": "Mus_musculus_kinase_substrate_network",
      "object": "Mus_musculus_kinase_substrate_network",
      "file": "Mus_musculus_kinase_substrate_network.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "source",
        "mor",
        "target",
        "likelihood"
      ],
      "rows": 25144,
      "table": true,
      "tojson": true
    },
    {
      "name": "swissProt",
      "title": "swissProt",
      "object": "swissProt",
      "file": "swissProt.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Entry",
        "Entry Name",
        "Protein names",
        "Gene Names",
        "Organism"
      ],
      "rows": 37532,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addZeroTime",
      "title": "Add Zero Timepoint Data to Treatment Subset",
      "topics": [
        "addZeroTime"
      ]
    },
    {
      "page": "calcKinaseScore",
      "title": "Calculate Kinase Activity Scores using 'decoupleR'",
      "topics": [
        "calcKinaseScore"
      ]
    },
    {
      "page": "checkRatioMat",
      "title": "Check the PP/FP ratio matrix and remove feature that do not meet requirements",
      "topics": [
        "checkRatioMat"
      ]
    },
    {
      "page": "clusterEnrich",
      "title": "Perform Cluster Enrichment Analysis",
      "topics": [
        "clusterEnrich"
      ]
    },
    {
      "page": "clusterTS",
      "title": "Perform Clustering on Time-Series Data",
      "topics": [
        "clusterTS"
      ]
    },
    {
      "page": "dda_example",
      "title": "dda_example",
      "topics": [
        "dda_example"
      ]
    },
    {
      "page": "dia_example",
      "title": "dia_example",
      "topics": [
        "dia_example"
      ]
    },
    {
      "page": "enrichDifferential",
      "title": "Perform Enrichment analysis on differentially expressed genes or phospho-sites",
      "topics": [
        "enrichDifferential"
      ]
    },
    {
      "page": "generateInputTable",
      "title": "Generate Input Table for Proteomic and Phosphoproteomic Analysis",
      "topics": [
        "generateInputTable"
      ]
    },
    {
      "page": "generateInputTable_DIA",
      "title": "Generate Input Table for DIA Analysis",
      "topics": [
        "generateInputTable_DIA"
      ]
    },
    {
      "page": "getDecouplerNetwork",
      "title": "Load Kinase-Substrate Interaction Network",
      "topics": [
        "getDecouplerNetwork"
      ]
    },
    {
      "page": "getOneSymbol",
      "title": "Extract the Last Gene Symbol from a Semicolon-Separated List",
      "topics": [
        "getOneSymbol"
      ]
    },
    {
      "page": "getRatioMatrix",
      "title": "Get Ratio Matrix of Phosphoproteome Data",
      "topics": [
        "getRatioMatrix"
      ]
    },
    {
      "page": "Homo_sapien_kinase_substrate_network",
      "title": "Homo_sapien_kinase_substrate_network",
      "topics": [
        "Homo_sapien_kinase_substrate_network"
      ]
    },
    {
      "page": "intensityBoxPlot",
      "title": "Plot Boxplot of Intensity Data",
      "topics": [
        "intensityBoxPlot"
      ]
    },
    {
      "page": "makeSmartPhosDirectory",
      "title": "Create SmartPhos Directory Structure",
      "topics": [
        "makeSmartPhosDirectory"
      ]
    },
    {
      "page": "medianNorm",
      "title": "Normalize a Matrix Using Median or Mean",
      "topics": [
        "medianNorm"
      ]
    },
    {
      "page": "mscale",
      "title": "Scale and Center a Matrix",
      "topics": [
        "mscale"
      ]
    },
    {
      "page": "Mus_musculus_kinase_substrate_network",
      "title": "Mus_musculus_kinase_substrate_network",
      "topics": [
        "Mus_musculus_kinase_substrate_network"
      ]
    },
    {
      "page": "normByFullProteome",
      "title": "Normalize Phosphoproteome by Full Proteome",
      "topics": [
        "normByFullProteome"
      ]
    },
    {
      "page": "performCombinedNormalization",
      "title": "Perform Combined Normalization on MultiAssayExperiment Data",
      "topics": [
        "performCombinedNormalization"
      ]
    },
    {
      "page": "performDifferentialExp",
      "title": "Perform Differential Expression Analysis",
      "topics": [
        "performDifferentialExp"
      ]
    },
    {
      "page": "plotAdjustmentResults",
      "title": "Plot Adjustment Results",
      "topics": [
        "plotAdjustmentResults"
      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Plot Heatmap of Intensity assay",
      "topics": [
        "plotHeatmap"
      ]
    },
    {
      "page": "plotIntensity",
      "title": "Plot Intensity Boxplots",
      "topics": [
        "plotIntensity"
      ]
    },
    {
      "page": "plotKinaseDE",
      "title": "Plot Kinase score for Differential Expression data",
      "topics": [
        "plotKinaseDE"
      ]
    },
    {
      "page": "plotKinaseTimeSeries",
      "title": "Plot Kinase Activity Time Series",
      "topics": [
        "plotKinaseTimeSeries"
      ]
    },
    {
      "page": "plotLogRatio",
      "title": "Plot Log Ratio of PP/FP (Phosphoproteome to Full Proteome) intensities",
      "topics": [
        "plotLogRatio"
      ]
    },
    {
      "page": "plotMissing",
      "title": "Plot Missing Data Completeness",
      "topics": [
        "plotMissing"
      ]
    },
    {
      "page": "plotPCA",
      "title": "Plot PCA",
      "topics": [
        "plotPCA"
      ]
    },
    {
      "page": "plotTimeSeries",
      "title": "Plot Time Series Data for a gene or phospho site from SummarizedExperiment object",
      "topics": [
        "plotTimeSeries"
      ]
    },
    {
      "page": "plotVolcano",
      "title": "Plot Volcano Plot for Differential Expression Analysis",
      "topics": [
        "plotVolcano"
      ]
    },
    {
      "page": "preprocessPhos",
      "title": "Preprocess Phosphoproteome Data",
      "topics": [
        "preprocessPhos"
      ]
    },
    {
      "page": "preprocessProteome",
      "title": "Preprocess Proteome Data",
      "topics": [
        "preprocessProteome"
      ]
    },
    {
      "page": "readExperiment",
      "title": "Read and Process the DDA experiment.",
      "topics": [
        "readExperiment"
      ]
    },
    {
      "page": "readExperimentDIA",
      "title": "Read and Process a DIA Experiment",
      "topics": [
        "readExperimentDIA"
      ]
    },
    {
      "page": "readOnePhos",
      "title": "Read and Filter Phosphorylation Data for a Specific Sample",
      "topics": [
        "readOnePhos"
      ]
    },
    {
      "page": "readOnePhosDIA",
      "title": "Read Phosphorylation Data for One Sample from DIA",
      "topics": [
        "readOnePhosDIA"
      ]
    },
    {
      "page": "readOneProteom",
      "title": "Read and Process One Proteomics Sample",
      "topics": [
        "readOneProteom"
      ]
    },
    {
      "page": "readOneProteomDIA",
      "title": "Read and Process a Single DIA Proteomics Sample",
      "topics": [
        "readOneProteomDIA"
      ]
    },
    {
      "page": "readPhosphoExperiment",
      "title": "Read Phosphorylation Experiment Data",
      "topics": [
        "readPhosphoExperiment"
      ]
    },
    {
      "page": "readPhosphoExperimentDIA",
      "title": "Read Phosphorylation Experiment Data from DIA",
      "topics": [
        "readPhosphoExperimentDIA"
      ]
    },
    {
      "page": "readProteomeExperiment",
      "title": "Read and Process Proteomics Experiment Data",
      "topics": [
        "readProteomeExperiment"
      ]
    },
    {
      "page": "readProteomeExperimentDIA",
      "title": "Read and Process a DIA Proteome Experiment",
      "topics": [
        "readProteomeExperimentDIA"
      ]
    },
    {
      "page": "runFisher",
      "title": "Perform Fisher's Exact Test on Gene Sets",
      "topics": [
        "runFisher"
      ]
    },
    {
      "page": "runGSEAforPhospho",
      "title": "Run GSEA for Phosphorylation Data",
      "topics": [
        "runGSEAforPhospho"
      ]
    },
    {
      "page": "runPhosphoAdjustment",
      "title": "Run Phospho Adjustment",
      "topics": [
        "runPhosphoAdjustment"
      ]
    },
    {
      "page": "runSmartPhos",
      "title": "Launch the SmartPhos Shiny Application",
      "topics": [
        "runSmartPhos"
      ]
    },
    {
      "page": "splineFilter",
      "title": "Filter Expression Matrix Using Spline Models",
      "topics": [
        "splineFilter"
      ]
    },
    {
      "page": "swissProt",
      "title": "swissProt",
      "topics": [
        "swissProt"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SmartPhos/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "askpass",
    "backports",
    "base64enc",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocManager",
    "BiocParallel",
    "bitops",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "caTools",
    "class",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "decoupleR",
    "DelayedArray",
    "dendextend",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "doRNG",
    "dplyr",
    "DT",
    "e1071",
    "ellipse",
    "emmeans",
    "estimability",
    "evaluate",
    "extraDistr",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "flashClust",
    "fontawesome",
    "foreach",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gmm",
    "gplots",
    "gridExtra",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "igraph",
    "impute",
    "imputeLCMD",
    "IRanges",
    "isoband",
    "iterators",
    "itertools",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "limma",
    "lme4",
    "lmtest",
    "magrittr",
    "marray",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "missForest",
    "modelr",
    "MsCoreUtils",
    "multcompView",
    "MultiAssayExperiment",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "norm",
    "numDeriv",
    "openssl",
    "otel",
    "parallelly",
    "pbkrtest",
    "pcaMethods",
    "pheatmap",
    "piano",
    "pillar",
    "pkgconfig",
    "plotly",
    "polynom",
    "preprocessCore",
    "proDA",
    "promises",
    "proxy",
    "purrr",
    "quantreg",
    "R6",
    "randomForest",
    "ranger",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "relations",
    "rlang",
    "rmarkdown",
    "rngtools",
    "rstatix",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sandwich",
    "sass",
    "scales",
    "scatterplot3d",
    "Seqinfo",
    "sets",
    "shiny",
    "shinyBS",
    "shinydashboard",
    "shinyjs",
    "shinythemes",
    "shinyWidgets",
    "slam",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "tmvtnorm",
    "urca",
    "utf8",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "visNetwork",
    "vsn",
    "withr",
    "xfun",
    "XML",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "SmartPhos_Shiny.Rmd",
      "filename": "SmartPhos_Shiny.html",
      "title": "SmartPhos Explorer: a one-stop data analysis platform for proteomic and phosphoproteomic data",
      "author": "Shubham Agrawal, Cong Quan Ta, Junyan Lu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Preprocessing tab",
        "Upload options",
        "fileTable.txt file",
        "Column annotations",
        "MultiAssayExperiment object",
        "Error checks",
        "Save and re-use the parsed dataset.",
        "Preprocessing options",
        "Other options",
        "Output",
        "PCA",
        "Heatmap",
        "Differential expression",
        "Time series clustering",
        "Other parameters for the analysis",
        "Enrichment analysis",
        "Kinase activity inference",
        "Time-series clustering",
        "Estimating kinase activity score",
        "Estimating kinase association",
        "Log Info",
        "Session Info",
        "References"
      ],
      "created": "2024-11-26 12:57:23",
      "modified": "2025-07-22 08:51:03",
      "commits": 11
    },
    {
      "source": "SmartPhos.Rmd",
      "filename": "SmartPhos.html",
      "title": "SmartPhos: a pipeline for processing and analysis of phosphoproteomic data",
      "author": "Shubham Agrawal, Junyan Lu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install and load SmartPhos Package",
        "Preprocessing the assay, basic visualization, PCA and Heatmaps",
        "Preprocessing options",
        "Different visualization options",
        "Differential Expression Analysis",
        "Time series clustering",
        "Enrichment analysis",
        "Gene Enrichment analysis on differential expression analysis results",
        "Gene Enrichment analysis on time-series results",
        "Phospho Enrichment analysis on time-series results",
        "Kinase Activity Inference",
        "Kinase activity inference on differential expression analysis results",
        "Session Info"
      ],
      "created": "2024-12-10 11:58:35",
      "modified": "2025-07-24 13:14:58",
      "commits": 15
    }
  ],
  "_score": 4.698970004336019,
  "_indexed": true,
  "_nocasepkg": "smartphos",
  "_universes": [
    "bioc",
    "shubh2565"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-30T09:59:57.000Z",
      "distro": "noble",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "41193e9434ef321ddfb93ac19f5bec1808a37b2d4d611fce084486244f3f1291",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-30T10:01:16.000Z",
      "distro": "noble",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "b23f3a9152a060f8df198d81a6f08b661eabc0a14d63fa0d7480e27ea96bdd1a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.0",
      "date": "2026-05-30T13:45:42.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "46bab2625a709490ecb3d314c4cd18b802d22b8d6d423a02a6f19bf533b63369",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.0",
      "date": "2026-05-30T13:46:04.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "48c5304016145ea0b2b41af43468c0cbbacb1cdcfe74767172f6f73a77f23490",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.0",
      "date": "2026-05-30T09:59:50.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "4956ac248a1ffa59e2511183aa3f1e3ae4c6a841fd4196700f816c44514ddf50",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:59:12.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "bad5301ab6b8cf41ef830b9c2a80cbe3cf226ad653fa5c713b8b2789dc41b05a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:58:26.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "294d72bf9096f4518a0d2a8f1246faf94874e11e5df351c189a270dce17824e6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:58:32.000Z",
      "commit": "fbaec544efe26887f16c395fc1bffe524eb9fc18",
      "fileid": "002110a503b626594dac13a131caac361cc0c463b2bc2b711df2f02b3e813cd9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676056037"
    }
  ]
}