{
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  "Package": "Rtpca",
  "Title": "Thermal proximity co-aggregation with R",
  "Version": "1.23.0",
  "Authors@R": "c(\nperson(\"Nils\", \"Kurzawa\", email = \"nilskurzawa@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"André\", \"Mateus\", role = c(\"aut\")),\nperson(\"Mikhail M.\", \"Savitski\", role = c(\"aut\")))",
  "Description": "R package for performing thermal proximity co-aggregation\nanalysis with thermal proteome profiling datasets to analyse\nprotein complex assembly and (differential) protein-protein\ninteractions across conditions.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "LazyData": "false",
  "biocViews": "Software, Proteomics, DataImport",
  "BugReports": "https://support.bioconductor.org/",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:04 UTC",
  "RemoteUrl": "https://github.com/bioc/Rtpca",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "Nils Kurzawa [aut, cre],\nAndré Mateus [aut],\nMikhail M. Savitski [aut]",
  "Maintainer": "Nils Kurzawa <nilskurzawa@gmail.com>",
  "MD5sum": "3c639656c07b098d6b5faddaafc2de2b",
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  "_published": "2026-07-03T11:56:50.917Z",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Rtpca",
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    "email": "nilskurzawa@gmail.com"
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      "package": "tidyr",
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      "package": "ggplot2",
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      "package": "knitr",
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  "_topics": [
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    "proteomics",
    "dataimport"
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    "type": "organization",
    "name": "Bioconductor",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
    "extra/Rtpca.html",
    "manual.pdf"
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  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CommonFeatures",
    "ComplexAnnotation",
    "ComplexBackgroundDistributionList",
    "ComplexRocTable",
    "ContrastCondName",
    "ContrastDistMat",
    "ContrastList",
    "createDistMat",
    "CtrlCondName",
    "diffTpcaResultTable",
    "DistMat",
    "DistMethod",
    "ObjList",
    "plotComplexRoc",
    "plotDiffTpcaVolcano",
    "plotPPiProfiles",
    "plotPPiRoc",
    "plotTpcaVolcano",
    "PPiAnnotation",
    "PPiRocTable",
    "PPiRocTableAnno",
    "runDiffTPCA",
    "runTPCA",
    "SetCommonFeatures",
    "SetComplexAnnotation",
    "SetComplexBackgroundDistributionList",
    "SetComplexRocTable",
    "SetContrastCondName",
    "SetContrastDistMat",
    "SetCtrlCondName",
    "SetDiffTpcaResultTable",
    "SetDistMat",
    "SetDistMethod",
    "SetPPiRocTable",
    "SetPPiRocTableAnno",
    "SetSummaryMethod",
    "SetTpcaResultTable",
    "SummaryMethod",
    "tpcaResult",
    "tpcaResultTable"
  ],
  "_datasets": [
    {
      "name": "ori_et_al_complex_ppis",
      "title": "Data frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900",
      "object": "ori_et_al_complex_ppis",
      "file": "ori_et_al_complex_ppis.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "complex_name",
        "x",
        "y",
        "pair",
        "combined_score"
      ],
      "rows": 8953,
      "table": true,
      "tojson": true
    },
    {
      "name": "ori_et_al_complexes_df",
      "title": "Data frame of annotated protein complexes by Ori et al.",
      "object": "ori_et_al_complexes_df",
      "file": "ori_et_al_complexes_df.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ensembl_id",
        "protein",
        "id"
      ],
      "rows": 2597,
      "table": true,
      "tojson": true
    },
    {
      "name": "string_ppi_df",
      "title": "Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700",
      "object": "string_ppi_df",
      "file": "string_ppi_df.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "x",
        "y",
        "combined_score",
        "pair"
      ],
      "rows": 252558,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CommonFeatures-tpcaResult-method",
      "title": "Extract CommonFeatures",
      "topics": [
        "CommonFeatures",
        "CommonFeatures,tpcaResult-method"
      ]
    },
    {
      "page": "ComplexAnnotation-tpcaResult-method",
      "title": "Extract ComplexAnnotation",
      "topics": [
        "ComplexAnnotation",
        "ComplexAnnotation,tpcaResult-method"
      ]
    },
    {
      "page": "ComplexBackgroundDistributionList-tpcaResult-method",
      "title": "Extract ComplexBackgroundDistributionList",
      "topics": [
        "ComplexBackgroundDistributionList",
        "ComplexBackgroundDistributionList,tpcaResult-method"
      ]
    },
    {
      "page": "ComplexRocTable-tpcaResult-method",
      "title": "Extract ComplexRocTable",
      "topics": [
        "ComplexRocTable",
        "ComplexRocTable,tpcaResult-method"
      ]
    },
    {
      "page": "ContrastCondName-tpcaResult-method",
      "title": "Extract ContrastCondName",
      "topics": [
        "ContrastCondName",
        "ContrastCondName,tpcaResult-method"
      ]
    },
    {
      "page": "ContrastDistMat-tpcaResult-method",
      "title": "Extract ContrastDistMat",
      "topics": [
        "ContrastDistMat",
        "ContrastDistMat,tpcaResult-method"
      ]
    },
    {
      "page": "ContrastList-tpcaResult-method",
      "title": "Extract ContrastList",
      "topics": [
        "ContrastList",
        "ContrastList,tpcaResult-method"
      ]
    },
    {
      "page": "createDistMat",
      "title": "Create distance matrix of all vs all protein melting profiles",
      "topics": [
        "createDistMat"
      ]
    },
    {
      "page": "CtrlCondName-tpcaResult-method",
      "title": "Extract CtrlCondName",
      "topics": [
        "CtrlCondName",
        "CtrlCondName,tpcaResult-method"
      ]
    },
    {
      "page": "diffTpcaResultTable-tpcaResult-method",
      "title": "Extract diffTpcaResultTable",
      "topics": [
        "diffTpcaResultTable",
        "diffTpcaResultTable,tpcaResult-method"
      ]
    },
    {
      "page": "DistMat-tpcaResult-method",
      "title": "Extract DistMat",
      "topics": [
        "DistMat",
        "DistMat,tpcaResult-method"
      ]
    },
    {
      "page": "DistMethod-tpcaResult-method",
      "title": "Extract DistMethod",
      "topics": [
        "DistMethod",
        "DistMethod,tpcaResult-method"
      ]
    },
    {
      "page": "ObjList-tpcaResult-method",
      "title": "Extract ObjList",
      "topics": [
        "ObjList",
        "ObjList,tpcaResult-method"
      ]
    },
    {
      "page": "ori_et_al_complex_ppis",
      "title": "Data frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900",
      "topics": [
        "ori_et_al_complex_ppis"
      ]
    },
    {
      "page": "ori_et_al_complexes_df",
      "title": "Data frame of annotated protein complexes by Ori et al.",
      "topics": [
        "ori_et_al_complexes_df"
      ]
    },
    {
      "page": "plotComplexRoc",
      "title": "Plot Complex ROC curve",
      "topics": [
        "plotComplexRoc"
      ]
    },
    {
      "page": "plotDiffTpcaVolcano",
      "title": "Plot differential TPCA analysis results",
      "topics": [
        "plotDiffTpcaVolcano"
      ]
    },
    {
      "page": "plotPPiProfiles",
      "title": "Plot thermal profile of protein pairs",
      "topics": [
        "plotPPiProfiles"
      ]
    },
    {
      "page": "plotPPiRoc",
      "title": "Plot PPI ROC curve",
      "topics": [
        "plotPPiRoc"
      ]
    },
    {
      "page": "plotTpcaVolcano",
      "title": "Plot TPCA analysis results",
      "topics": [
        "plotTpcaVolcano"
      ]
    },
    {
      "page": "PPiAnnotation-tpcaResult-method",
      "title": "Extract PPiAnnotation",
      "topics": [
        "PPiAnnotation",
        "PPiAnnotation,tpcaResult-method"
      ]
    },
    {
      "page": "PPiRocTable-tpcaResult-method",
      "title": "Extract PPiRocTable",
      "topics": [
        "PPiRocTable",
        "PPiRocTable,tpcaResult-method"
      ]
    },
    {
      "page": "PPiRocTableAnno-tpcaResult-method",
      "title": "Extract PPiRocTableAnno",
      "topics": [
        "PPiRocTableAnno",
        "PPiRocTableAnno,tpcaResult-method"
      ]
    },
    {
      "page": "runDiffTPCA",
      "title": "Run differential TPCA analysis",
      "topics": [
        "runDiffTPCA"
      ]
    },
    {
      "page": "runTPCA",
      "title": "Run the TPCA analysis",
      "topics": [
        "runTPCA"
      ]
    },
    {
      "page": "SetCommonFeatures-tpcaResult-method",
      "title": "Set CommonFeatures",
      "topics": [
        "SetCommonFeatures",
        "SetCommonFeatures,tpcaResult-method"
      ]
    },
    {
      "page": "SetComplexAnnotation-tpcaResult-method",
      "title": "Set ComplexAnnotation",
      "topics": [
        "SetComplexAnnotation",
        "SetComplexAnnotation,tpcaResult-method"
      ]
    },
    {
      "page": "SetComplexBackgroundDistributionList-tpcaResult-method",
      "title": "Set ComplexBackgroundDistributionList",
      "topics": [
        "SetComplexBackgroundDistributionList",
        "SetComplexBackgroundDistributionList,tpcaResult-method"
      ]
    },
    {
      "page": "SetComplexRocTable-tpcaResult-method",
      "title": "Set ComplexRocTable",
      "topics": [
        "SetComplexRocTable",
        "SetComplexRocTable,tpcaResult-method"
      ]
    },
    {
      "page": "SetContrastCondName-tpcaResult-method",
      "title": "Set ContrastCondName",
      "topics": [
        "SetContrastCondName",
        "SetContrastCondName,tpcaResult-method"
      ]
    },
    {
      "page": "SetContrastDistMat-tpcaResult-method",
      "title": "Set ContrastDistMat",
      "topics": [
        "SetContrastDistMat",
        "SetContrastDistMat,tpcaResult-method"
      ]
    },
    {
      "page": "SetCtrlCondName-tpcaResult-method",
      "title": "Set CtrlCondName",
      "topics": [
        "SetCtrlCondName",
        "SetCtrlCondName,tpcaResult-method"
      ]
    },
    {
      "page": "SetDiffTpcaResultTable-tpcaResult-method",
      "title": "Set diffTpcaResultTable",
      "topics": [
        "SetDiffTpcaResultTable",
        "SetDiffTpcaResultTable,tpcaResult-method"
      ]
    },
    {
      "page": "SetDistMat-tpcaResult-method",
      "title": "Set DistMat",
      "topics": [
        "SetDistMat",
        "SetDistMat,tpcaResult-method"
      ]
    },
    {
      "page": "SetDistMethod-tpcaResult-method",
      "title": "Set distMethod",
      "topics": [
        "SetDistMethod",
        "SetDistMethod,tpcaResult-method"
      ]
    },
    {
      "page": "SetPPiRocTable-tpcaResult-method",
      "title": "Set PPiRocTable",
      "topics": [
        "SetPPiRocTable",
        "SetPPiRocTable,tpcaResult-method"
      ]
    },
    {
      "page": "SetPPiRocTableAnno-tpcaResult-method",
      "title": "Set PPiRocTableAnno",
      "topics": [
        "SetPPiRocTableAnno",
        "SetPPiRocTableAnno,tpcaResult-method"
      ]
    },
    {
      "page": "SetSummaryMethod-tpcaResult-method",
      "title": "Set summaryMethod",
      "topics": [
        "SetSummaryMethod",
        "SetSummaryMethod,tpcaResult-method"
      ]
    },
    {
      "page": "SetTpcaResultTable-tpcaResult-method",
      "title": "Set TpcaResultTable",
      "topics": [
        "SetTpcaResultTable",
        "SetTpcaResultTable,tpcaResult-method"
      ]
    },
    {
      "page": "string_ppi_df",
      "title": "Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700",
      "topics": [
        "string_ppi_df"
      ]
    },
    {
      "page": "SummaryMethod-tpcaResult-method",
      "title": "Extract SummaryMethod",
      "topics": [
        "SummaryMethod",
        "SummaryMethod,tpcaResult-method"
      ]
    },
    {
      "page": "tpcaResult-class",
      "title": "S4 TPCA Result Class",
      "topics": [
        "tpcaResult",
        "tpcaResult-class"
      ]
    },
    {
      "page": "tpcaResultTable-tpcaResult-method",
      "title": "Extract tpcaResultTable",
      "topics": [
        "tpcaResultTable",
        "tpcaResultTable,tpcaResult-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Rtpca/raw/HEAD/README.md",
  "_rundeps": [
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    "BiocGenerics",
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "fdrtool",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "pROC",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Rtpca.Rmd",
      "filename": "Rtpca.html",
      "title": "Introduction to Rtpca",
      "author": "Nils Kurzawa",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "The Rtpca package workflow",
        "Import Thermal proteome profiling data using the TPP package",
        "Performing thermal co-aggregation analysis with Rtpca",
        "Run TPCA on data from a single condition",
        "Run differential TPCA on two conditions",
        "Additional remarks",
        "Acknowledgements",
        "References"
      ],
      "created": "2019-12-13 14:13:42",
      "modified": "2020-11-27 13:22:28",
      "commits": 21
    }
  ],
  "_score": 4.681241237375588,
  "_indexed": true,
  "_nocasepkg": "rtpca",
  "_universes": [
    "bioc"
  ],
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      "r": "4.5.3",
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      "fileid": "302029b4bf862dbc6ea3507d7e5c6c1c0c7eb3f97a8b2a07f8f0e758bf56a5b7",
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