Chapter 1 Introduction

This is a tutorial introducing the analysis of microbiome functional data.

Flowchart of this tutorial:

Flowchart

MGS data of one MAFLD cohorts was used as demo data throughout the first 6 chapters in this tutorial.

8 MGS samples of 4 patients from 2 groups in MAFLD projects were used as Demo data.

16S data of mouse fecal samples from BeiZhong E round project was used as demo data in Chapter 8 (PICRUSt2).

Notably, only Genus names should be used as input in Chapter 7 for MSEA analysis.

This book includes 6 Chapters of the following 5 modules on funcitonal analysis:

5 modules include:

  • Analysis of Metacyc data

  • Analysis of KEGG data

  • Analysis of target database data

  • MSEA

  • PICRUSt2

6 Chapters include:

  • Chapter1, introducing basic information of this tutorial.

  • Chapter2, introducing the analysis of Metacyc data.

  • Chapter3, introducing the analysis of processed KEGG data.

  • Chapter4, introducing the analysis of processed target database (use CARD as example) data.

  • Chapter5, introducing MSEA.

  • Chapter6, introducing PICRUSt2 analysis of 16S data.