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Code and partial data repository for the manuscript entitled Comprehensive Analytical Approaches for Integrating Multiple Microbiome Studies by Fu et al..

Developed and maintained by: Chenlian (Tom) Fu
Advised by: Dr. Wodan Ling
Affiliations: Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center

This github repository stores the code for the data integration pipeline as described in the manuscript, which includes data generation as well as the execution and evaluations of microbiome cross-study data integration methods. The goal of this repository are to enable readers to reproduce the analyses done in the paper as well as leveraging their own data along with the provided code to decide which data integration method they wish to use for their own analyses. Our pipeline consists of three steps:

• Data generation/collection
• Running data integration (batch correction) methods on datasets to corrected data
• Evaluation of the methods

Table of content

• 0. Environment set up
• 1. (Simulated) Data generation/ (real-world data) collection
  • 1.1 Simulation data generation
  • 1.2 Real world microbiome data collection and cleaning
• 2. Running/executing methods
  • 2.1 For methods implemented in R
    • 2.1.1 Running these methods for simulation
    • 2.1.2 Running these methods for real-world datasets
  • 2.2 For methods implemented in Python
    • 2.2.1 Running these methods for simulation
    • 2.2.2 Running these methods for real-world datasets
• 3. Evaluation
  • 3.1 Generating summary statistics for each simulated dataset or for each real-world dataset
    • 3.1.1 Summary stats for simulated datasets
    • 3.1.2 Summary stats for real-world datasets
  • 3.2 Generating intuitive visualizations based on the summary statistics
• 3. Evaluation
  • 3.1 Generating summary statistics for each simulated dataset or for each real-world dataset
    • 3.1.1 Summary stats for simulated datasets
    • 3.1.2 Summary stats for real-world datasets
  • 3.2 Generating intuitive visualizations based on the summary statistics