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  "Title": "Reproduce figures in IHW paper",
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  "Description": "This package conveniently wraps all functions needed to\nreproduce the figures in the IHW paper\n(https://www.nature.com/articles/nmeth.3885) and the data\nanalysis in\nhttps://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf.\nthe arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it\nis a companion package to the Bioconductor IHW package.",
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        "analyze_dataset"
      ]
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      "topics": [
        "bh"
      ]
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      "title": "ddhf: Greedy independent filtering",
      "topics": [
        "ddhf"
      ]
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    {
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      "title": "t-test simulation: Simulate rowwise t-tests",
      "topics": [
        "du_ttest_sim",
        "du_ttest_sim_fun"
      ]
    },
    {
      "page": "gbh",
      "title": "gbh: Grouped Benjamini Hochberg",
      "topics": [
        "gbh",
        "lsl_gbh",
        "tst_gbh"
      ]
    },
    {
      "page": "ihw_naive",
      "title": "IHW wrappers",
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        "ihw_5fold_reg",
        "ihw_bonf_5fold_reg",
        "ihw_ecdf_5fold",
        "ihw_naive",
        "ihw_storey_5fold"
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      "title": "Null simulation: Generate uniformly distributed p-values and covariates",
      "topics": [
        "null_sim",
        "null_sim_fun"
      ]
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      "page": "pretty_legend",
      "title": "helper function to create nice legends",
      "topics": [
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      ]
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      "topics": [
        "run_evals"
      ]
    },
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      "topics": [
        "scott_fdrreg"
      ]
    },
    {
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      "topics": [
        "storey_qvalue"
      ]
    },
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      "topics": [
        "stratified_bh"
      ]
    },
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      "title": "Normal PRDS simulation: Covariate is effect size under alternative, there are latent factors driving PRDS correlations among hypotheses",
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        "wasserman_normal_prds_sim_fun"
      ]
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      "title": "Normal simulation: Covariate is effect size under alternative",
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        "wasserman_normal_sim_fun"
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      "author": "Nikos Ignatiadis",
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      "author": "Nikos Ignatiadis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Panel a)",
        "Panel b)",
        "Proteomics Example",
        "panel c)",
        "Panel d)",
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        "Load in data",
        "Panel e)",
        "Panel f)",
        "Put all panels together for main fig!",
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      "author": "Nikos Ignatiadis",
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      "headings": [
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        "Data for panels a,b",
        "Panel a)",
        "Panel b)",
        "Panels a, b)",
        "Panels c, d)",
        "Data for panels c,d)",
        "Panel c)",
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        "Put panels c), d) together:",
        "Panels e),f)",
        "Load data for panels e),f)",
        "Panel e)",
        "Panel f)",
        "Combine main panels for size investing",
        "Combine everything into main text simulation figure",
        "New main fig sim. figures without borders:",
        "Supplementary panel b)",
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      "author": "Nikos Ignatiadis",
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