Chapter 1 Prerequisites

Here, we give users one example to practice the MGS microbiota data analysis workflow by XMAS 2.0. By the way, we also recommend users handling your own microbiota data in a reasonable manner when you utilize this package or workflow. Pay attention to whether your data fit the methods this package provided.

1.1 Preparing for the tutorial

This tutorial requires that the users should have basic knowledge on R language and statistics. If you are new to microbial research, we recommend the Statistical Analysis of Microbiome Data with R (Xia et al. 2018) as guide book.

We suggest users using local laptop because our own server have not deployed XMAS 2.0 package yet. In addition, installing the following software before using XMAS 2.0.

1.2 Workflow description

The standard data analysis of 16S and MGS data by XMAS 2.0. The upstream process is performed by in-house pipeline. and this example just shows how to perform downstream data analysis. In briefly, the example comprises the following steps:

  1. Converting inputs into phyloseq object;

  2. Quality Evaluation;

  3. Pre-Processing Data;

  4. Diversity analysis;

  5. Ordination analysis;

  6. Composition analysis;

  7. Differential analysis.

Functions of XMAS 2.0

Figure 1.1: Functions of XMAS 2.0


Xia, Yinglin, Jun Sun, Ding-Geng Chen, et al. 2018. Statistical Analysis of Microbiome Data with r. Vol. 847. Springer.