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        "From counts",
        "Outlier Identification",
        "Visualization and Summary Plots",
        "Adding Custom Layers to Boxplots",
        "Model Proportions Directly (e.g. from deconvolution)",
        "Continuous Factor Analysis",
        "Random Effect Modeling (Mixed-Effect Modeling)",
        "Random Intercept Model",
        "Random Effect Model (random slopes)",
        "Nested Random Effects",
        "Result Interpretation and Communication",
        "Contrasts Analysis",
        "Categorical Factor Analysis (Bayesian ANOVA)",
        "Differential Variability Analysis",
        "Recommended Settings for Different Data Types",
        "For Single-Cell RNA Sequencing",
        "For CyTOF and Microbiome Data",
        "MCMC Chain Visualization"
      ],
      "created": "2021-09-19 08:11:10",
      "modified": "2026-07-21 06:32:31",
      "commits": 48
    },
    {
      "source": "splines.Rmd",
      "filename": "splines.html",
      "title": "Smooth (spline) terms in sccomp",
      "author": "Stefano Mangiola",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why smooth terms?",
        "What is supported",
        "Continuous covariate",
        "1. Fit ~ type + s(pseudotime, k = 5)",
        "2. Visualise the curve",
        "3. Let's use a smaller basis (k = 3)",
        "4. Under the hood: What s() actually decomposes into",
        "Hierarchical smooths: per-group curves with shared structure",
        "1. Fit ~ s(pseudotime, tissue, bs = \"fs\", k = 5)",
        "2. Predict and plot per-tissue curves",
        "fs vs s(x, by = tissue)",
        "Multiple smooths and mixing with random effects",
        "Session info"
      ],
      "created": "2026-07-15 00:51:37",
      "modified": "2026-07-22 01:19:35",
      "commits": 2
    }
  ],
  "_score": 9.53911149360587,
  "_indexed": true,
  "_nocasepkg": "sccomp",
  "_universes": [
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    "mangiolalaboratory"
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