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  "Title": "Simple Transcriptome Meta-Analysis for Identifying\nStress-Responsive Genes",
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  "Author": "Yusuke Fukuda [aut, cre], Atsushi Fukushima [aut]",
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  "Description": "Stress Response score (SRscore) is a stress responsiveness\nmeasure for transcriptome datasets and is based on the\nvote-counting method. The SRscore is determined to evaluate and\nscore genes on the basis of the consistency of the direction of\ntheir regulation (Up-regulation, Down-regulation, or No change)\nunder stress conditions across multiple analyzed research\nprojects. This package is based on the HN-score (score based on\nthe ratio of gene expression between hypoxic and normoxic\nconditions) proposed by Tamura and Bono (2022)\n<doi:10.3390/life12071079>, and can calculate both the original\nmethod and an extended calculation method described in Fukuda\net al. (2025) <doi:10.1093/plphys/kiaf105>.",
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  "Repository": "https://fusk-kpu.r-universe.dev",
  "Date/Publication": "2026-03-24 11:20:50 UTC",
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    "calcSRscore",
    "directly_calcSRscore",
    "expand_by_group",
    "find_diffexp",
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    {
      "page": "calcSRratio",
      "title": "Calculate the Stress Response ratio (SRratio)",
      "topics": [
        "calcSRratio"
      ]
    },
    {
      "page": "calcSRscore",
      "title": "Create a Data Frame of SRscore",
      "topics": [
        "calcSRscore"
      ]
    },
    {
      "page": "directly_calcSRscore",
      "title": "Aggregate the results of the three functions into a single list",
      "topics": [
        "directly_calcSRscore"
      ]
    },
    {
      "page": "expand_by_group",
      "title": "Create a data frame from all combinations between two specified variables within each group",
      "topics": [
        "expand_by_group"
      ]
    },
    {
      "page": "find_diffexp",
      "title": "Find the expression ratio for each experimental sample for the specified gene.",
      "topics": [
        "find_diffexp"
      ]
    },
    {
      "page": "HNscore",
      "title": "Reproducing HN-scores from HN-ratios Using the SRscore Package",
      "topics": [
        "HNscore"
      ]
    },
    {
      "page": "logHNratioHypoxia",
      "title": "Reproducing HN-scores from HN-ratios Using the SRscore Package",
      "topics": [
        "logHNratioHypoxia"
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    },
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      "title": "Metadata of abscisic acid stress microarray dataset in _Arabidopsis thaliana_",
      "topics": [
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    {
      "page": "MetadataHypoxia",
      "title": "Metadata of Hypoxia stress RNA-Seq dataset in _Arabidopsis thaliana_",
      "topics": [
        "MetadataHypoxia"
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    },
    {
      "page": "plot_SRscore_distr",
      "title": "Plot the Distribution of SRscore Values",
      "topics": [
        "plot_SRscore_distr"
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    },
    {
      "page": "plot_SRscore_rank",
      "title": "Plot Ranked SRscore Values with Threshold-Based Highlighting",
      "topics": [
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    },
    {
      "page": "plot_SRscore_top",
      "title": "Barplot of Top Genes Ranked by Absolute SRscore",
      "topics": [
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      "title": "Test data for calculating SRratio using sample data",
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      "page": "SRscore_test",
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    {
      "page": "TPMHypoxia",
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        "TPMHypoxia"
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    },
    {
      "page": "TranscriptomeABA",
      "title": "Abscisic acid stress microarray dataset in _Arabidopsis thaliana_",
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  "_vignettes": [
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      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "SRscore Package Vignette",
      "author": "Yusuke Fukuda",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Functions Overview",
        "Demonstration datasets",
        "MetadataABA",
        "TranscriptomeABA",
        "SRGA (Stress Responsive Gene Atlas)",
        "Example Workflow",
        "1. Comparison Pairs",
        "2. Calculation of the SRratio",
        "3. Calculate SRscore",
        "Simple Plotting",
        "SRscore distribution",
        "Ranked SRscore",
        "Top SRscore",
        "All-in-One Execution",
        "Metadata viewer",
        "Downstream analysis",
        "Enrichment Analysis",
        "Heatmap",
        "Template Matching",
        "Summary",
        "Session info",
        "References"
      ],
      "created": "2025-04-27 07:46:13",
      "modified": "2026-02-06 04:21:08",
      "commits": 12
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