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  "Title": "Microbiome differential abudance and correlation analyses with\nbias correction",
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  "Description": "ANCOMBC is a package containing differential abundance\n(DA) and correlation analyses for microbiome data.\nSpecifically, the package includes Analysis of Compositions of\nMicrobiomes with Bias Correction 2 (ANCOM-BC2), Analysis of\nCompositions of Microbiomes with Bias Correction (ANCOM-BC),\nand Analysis of Composition of Microbiomes (ANCOM) for DA\nanalysis, and Sparse Estimation of Correlations among\nMicrobiomes (SECOM) for correlation analysis. Microbiome data\nare typically subject to two sources of biases: unequal\nsampling fractions (sample-specific biases) and differential\nsequencing efficiencies (taxon-specific biases). Methodologies\nincluded in the ANCOMBC package are designed to correct these\nbiases and construct statistically consistent estimators.",
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        "6.7 ANCOM-BC2 pattern analysis",
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        "4.2 Visualizations",
        "Pearson correlation with thresholding",
        "Pearson correlation with p-value filtering",
        "Distance correlation with p-value filtering",
        "4.3 Run secom functions using the tse object",
        "4.4 Run secom functions by directly providing the abundance and metadata",
        "5. Run SECOM on Multiple Ecosystems",
        "5.1 Data manipulation",
        "5.2 Run secom functions using the phyloseq object",
        "5.3 Visualizations",
        "5.4 Run secom functions using the tse object",
        "5.5 Run secom functions by directly providing the abundance and metadata",
        "Session information",
        "References"
      ],
      "created": "2022-10-11 02:38:02",
      "modified": "2025-01-07 23:59:55",
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    {
      "source": "data_sanity_check.Rmd",
      "filename": "data_sanity_check.html",
      "title": "Tutorial on Data Sanity and Integrity Checks",
      "author": "Menglu Liang$^1$, Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Installation",
        "3. Examples",
        "3.1 Import a phyloseq object",
        "3.2 Import a tse object",
        "3.3 Import a matrix or data.frame",
        "Session information",
        "References"
      ],
      "created": "2024-10-21 16:17:11",
      "modified": "2025-03-16 14:52:53",
      "commits": 2
    }
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