{
  "_id": "6a60a330c766cc6deb6aa07d",
  "Package": "TraianProt",
  "Title": "TraianProt: a user-friendly R package for wide format proteomics\ndata downstream analysis",
  "Version": "0.99.16",
  "Authors@R": "person(\"Samuel\", \"de la Camara Fuentes\", , \"sdelacam@ucm.es\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-6718-5896\"))",
  "Description": "A proteomics data analysis platform that enables the\nanalysis of both label-free and labeled data from\nData-Dependent or Data-Independent Acquisition mass\nspectrometry mode, supporting MaxQuant, MSFragger, DIA-NN,\nProteoScape, and Proteome Discoverer output formats. TraianProt\nprovides a comprehensive suite of stepwise downstream analysis\nmodules, which includes data filtering, normalization\nprocedures, and missing value imputation strategies. The\nplatform also incorporates robust statistical frameworks for\ndifferential expression testing, with peptide-spectrum match\nlevel correction, thereby enhancing the reliability of\nbiological interpretations.",
  "License": "GPL (>= 3)",
  "biocViews": "Software, Proteomics, MassSpectrometry, DataImport,\nNormalization, DifferentialExpression, GO",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/SamueldelaCamaraFuentes/TraianProt",
  "BugReports": "https://github.com/SamueldelaCamaraFuentes/TraianProt/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-16 13:27:26 UTC",
  "RemoteUrl": "https://github.com/bioc/TraianProt",
  "RemoteRef": "HEAD",
  "RemoteSha": "ee5dcc08bcf0976549253d10d63ac4602392a46f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-22 10:51:21 UTC",
    "User": "root"
  },
  "Author": "Samuel de la Camara Fuentes [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6718-5896>)",
  "Maintainer": "Samuel de la Camara Fuentes <sdelacam@ucm.es>",
  "_user": "bioc",
  "_type": "src",
  "_file": "TraianProt_0.99.16.tar.gz",
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  "_sha256": "c4566284a5929dc3261ba64a8f438ee9e98ea34607cd9c2bc36478f41c5c7421",
  "_expires": "2026-10-30T11:02:06.000Z",
  "_created": "2026-07-22T10:51:21.000Z",
  "_published": "2026-07-22T11:02:08.575Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 4
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29913082485",
  "_status": "success",
  "_upstream": "https://github.com/bioc/TraianProt",
  "_commit": {
    "id": "ee5dcc08bcf0976549253d10d63ac4602392a46f",
    "author": "Samuel <123367287+SamueldelaCamaraFuentes@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Revise installation instructions for TraianProt\n\nUpdated installation instructions for TraianProt R package to use BiocManager.",
    "time": 1784208446
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  "_maintainer": {
    "name": "Samuel de la Camara Fuentes",
    "email": "sdelacam@ucm.es",
    "orcid": "0000-0001-6718-5896"
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  "_dependencies": [
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      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggExtra",
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    },
    {
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    },
    {
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    },
    {
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    {
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    },
    {
      "package": "wrMisc",
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    {
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    {
      "package": "BiocStyle",
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  "_owner": "bioc",
  "_selfowned": true,
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  "_updates": [
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  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.16",
      "bioc": "3.24"
    }
  ],
  "_topics": [
    "software",
    "proteomics",
    "massspectrometry",
    "dataimport",
    "normalization",
    "differentialexpression",
    "go",
    "dia-nn",
    "mass-spectrometry",
    "maxquant",
    "msfragger",
    "proteome-discoverer",
    "proteomics-data-analysis"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "samueldelacamarafuentes",
      "count": 164,
      "uuid": 123367287
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 450,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/samueldelacamarafuentes/traianprot",
  "_rbuild": "4.6.1",
  "_assets": [
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    "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/TraianProt.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "barplot_func",
    "boxplot_function",
    "collapse_technical_replicates",
    "corrplot_function",
    "Diferential_boxplot",
    "dotplot_func",
    "filter_valids",
    "gostplot_func",
    "Goterms_finder",
    "histogram",
    "identify_proteins",
    "igraph_analysis",
    "impute_data",
    "impute_KNN_data",
    "interactions_down",
    "interactions_up",
    "median_centering",
    "my_heatmap",
    "my_heatmap_differential",
    "normalization_func",
    "obtain_LOG.names",
    "obtain_unique_proteins",
    "pca",
    "plotCV2",
    "postimputation_state",
    "preimputation_state",
    "qqplot_function",
    "quick_filtering",
    "runTraianProt",
    "scatterplot_function",
    "statistical_analysis",
    "traian_to_SE",
    "traianprot_power_curve",
    "tsne",
    "unique_peptides_filter",
    "venn_diagram",
    "volcano_plot",
    "volcano_plot_tiff"
  ],
  "_help": [
    {
      "page": "barplot_func",
      "title": "Create Bar Plot from Enrichment Results",
      "topics": [
        "barplot_func"
      ]
    },
    {
      "page": "boxplot_function",
      "title": "Create Boxplot of Sample Intensities",
      "topics": [
        "boxplot_function"
      ]
    },
    {
      "page": "collapse_technical_replicates",
      "title": "Collapse Technical Replicates in Proteomics Data",
      "topics": [
        "collapse_technical_replicates"
      ]
    },
    {
      "page": "corrplot_function",
      "title": "Correlation Matrix",
      "topics": [
        "corrplot_function"
      ]
    },
    {
      "page": "Diferential_boxplot",
      "title": "Differential Protein Boxplot",
      "topics": [
        "Diferential_boxplot"
      ]
    },
    {
      "page": "dotplot_func",
      "title": "Create Dot Plot from Enrichment Results",
      "topics": [
        "dotplot_func"
      ]
    },
    {
      "page": "filter_valids",
      "title": "Filter proteins by valid values",
      "topics": [
        "filter_valids"
      ]
    },
    {
      "page": "gostplot_func",
      "title": "Manhattan Plot for Functional Enrichment",
      "topics": [
        "gostplot_func"
      ]
    },
    {
      "page": "Goterms_finder",
      "title": "Find GO Terms (gprofiler2)",
      "topics": [
        "Goterms_finder"
      ]
    },
    {
      "page": "histogram",
      "title": "Plot a Histogram",
      "topics": [
        "histogram"
      ]
    },
    {
      "page": "identify_proteins",
      "title": "Identify Proteins",
      "topics": [
        "identify_proteins"
      ]
    },
    {
      "page": "igraph_analysis",
      "title": "Perform igraph Analysis on STRING Subnetworks",
      "topics": [
        "igraph_analysis"
      ]
    },
    {
      "page": "impute_data",
      "title": "Impute Missing Values using Down-Shifted Normal Distribution",
      "topics": [
        "impute_data"
      ]
    },
    {
      "page": "impute_KNN_data",
      "title": "Impute missing data using k-NN",
      "topics": [
        "impute_KNN_data"
      ]
    },
    {
      "page": "interactions_down",
      "title": "Plot STRING Interactions for Down-regulated Proteins",
      "topics": [
        "interactions_down"
      ]
    },
    {
      "page": "interactions_up",
      "title": "Get STRING Interactions for Up-regulated Proteins",
      "topics": [
        "interactions_up"
      ]
    },
    {
      "page": "median_centering",
      "title": "Perform median centering normalization",
      "topics": [
        "median_centering"
      ]
    },
    {
      "page": "my_heatmap",
      "title": "Base R Heatmap",
      "topics": [
        "my_heatmap"
      ]
    },
    {
      "page": "my_heatmap_differential",
      "title": "Differential Protein Heatmap (ggplot)",
      "topics": [
        "my_heatmap_differential"
      ]
    },
    {
      "page": "normalization_func",
      "title": "Apply Normalization to LOG2 Columns",
      "topics": [
        "normalization_func"
      ]
    },
    {
      "page": "obtain_LOG.names",
      "title": "Obtain LOG2 Column Names",
      "topics": [
        "obtain_LOG.names"
      ]
    },
    {
      "page": "obtain_unique_proteins",
      "title": "Obtain Unique Proteins Between Conditions",
      "topics": [
        "obtain_unique_proteins"
      ]
    },
    {
      "page": "pca",
      "title": "Custom PCA Plot (Base R)",
      "topics": [
        "pca"
      ]
    },
    {
      "page": "plotCV2",
      "title": "Plot Coefficient of Variation vs. Mean",
      "topics": [
        "plotCV2"
      ]
    },
    {
      "page": "postimputation_state",
      "title": "Plot Post-Imputation Density",
      "topics": [
        "postimputation_state"
      ]
    },
    {
      "page": "preimputation_state",
      "title": "Plot Missingness Pattern",
      "topics": [
        "preimputation_state"
      ]
    },
    {
      "page": "qqplot_function",
      "title": "Create a Q-Q Plot",
      "topics": [
        "qqplot_function"
      ]
    },
    {
      "page": "quick_filtering",
      "title": "Quick Data Filtering",
      "topics": [
        "quick_filtering"
      ]
    },
    {
      "page": "runTraianProt",
      "title": "Launch the TraianProt Shiny Application",
      "topics": [
        "runTraianProt"
      ]
    },
    {
      "page": "scatterplot_function",
      "title": "Create a Scatterplot with Marginal Densities",
      "topics": [
        "scatterplot_function"
      ]
    },
    {
      "page": "statistical_analysis",
      "title": "Limma function for statistical analysis",
      "topics": [
        "statistical_analysis"
      ]
    },
    {
      "page": "traian_to_SE",
      "title": "Export TraianProt results to SummarizedExperiment",
      "topics": [
        "traian_to_SE"
      ]
    },
    {
      "page": "traianprot_power_curve",
      "title": "Create power curve",
      "topics": [
        "traianprot_power_curve"
      ]
    },
    {
      "page": "tsne",
      "title": "t-SNE Plot",
      "topics": [
        "tsne"
      ]
    },
    {
      "page": "unique_peptides_filter",
      "title": "Filter Proteins by Unique Peptide Counts",
      "topics": [
        "unique_peptides_filter"
      ]
    },
    {
      "page": "venn_diagram",
      "title": "Create a Venn Diagram",
      "topics": [
        "venn_diagram"
      ]
    },
    {
      "page": "volcano_plot",
      "title": "This function generates an interactive volcano plot using the 'plotly' package based on differential expression results.",
      "topics": [
        "volcano_plot"
      ]
    },
    {
      "page": "volcano_plot_tiff",
      "title": "Create a Static Volcano Plot for Publication",
      "topics": [
        "volcano_plot_tiff"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/TraianProt/raw/HEAD/README.md",
  "_rundeps": [
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    "AnnotationDbi",
    "ape",
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    "globals",
    "glue",
    "GO.db",
    "GOSemSim",
    "gplots",
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    "gridExtra",
    "gridGraphics",
    "gson",
    "gsubfn",
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    "gtools",
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    "htmltools",
    "htmlwidgets",
    "httpuv",
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    "jquerylib",
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    "KEGGREST",
    "KernSmooth",
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    "MASS",
    "Matrix",
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