milk

Contents:

  • Installation
    • Option 1: Pre-compiled binary (Recommended)
    • Option 2: MILK installation as a Julia module
    • Verify successful installation
  • Usage
    • Example usage
    • Input
    • Output
    • MILK heuristics
    • High Performance Computing mode
  • Tutorials
    • MILK tutorial: Network visualization of MILK trees PBMC (3k dataset)
      • Importing libraries
      • Loading the dataset
      • MILK input
      • MILK execution
        • Exporting MILK directory to PATH
      • Visualization of the single-cell MILK tree embedding
    • MILK tutorial: Quantifying dynamic cellular information with MILK trees (Paul15 dataset)
      • Overview
      • Importing libraries
      • Loading the dataset
      • Standard pre-processing
      • MILK input
      • Running MILK
      • Processing the MILK output
      • Visualizing the MILK tree in R (ggraph package)
      • Downstream analyses utilizing the MILK tree output
        • Weighted average depth of each cell type in the MILK tree
        • Calculating the number of (productive) branching events from each cell (leaf) to the root
        • Threshold-based quantification cell type substructure in the MILK tree topology
milk
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© Copyright 2026, Brett Kiyota.

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