Bioinformatic and Statistical Analysis of Microbiome Data

✍ Scribed by Youngchul Kim

• Publisher: Springer
• Tongue: English
• Leaves: 47
• Category: Library

✦ Table of Contents

Chapter 10: Bioinformatic and Statistical Analysis of Microbiome Data
1 Introduction
2 Datasets Used to Illustrate the Methods
3 Bioinformatic and Statistical Methods for Microbiome Data Analysis
3.1 Overview of Bioinformatic Pipeline for Raw Sequencing Data Analysis
3.2 Bioinformatic Analysis of Marker-Gene Sequencing Data
3.2.1 Sequencing Error Control and Variant Call
3.2.2 Taxonomic Classification
3.2.3 Phylogenetic Tree Construction
3.3 Bioinformatic Analysis of Metagenome Shotgun Sequencing Data
3.3.1 Quality Control and Decontamination
3.3.2 Reference-Based Taxonomy Identification
3.3.3 Reference-Based Functional Classification
3.3.4 De Novo Metagenomic Assembly Analysis
3.4 Statistical Analysis of Microbiome Data
3.4.1 Structure of Microbiome Data
3.4.2 Property of Microbiome Data
3.4.3 Quality Control of Microbiome Data
3.4.4 Normalization of Microbiome Data
3.4.5 Exploratory Analysis of Microbiome Data
3.4.6 Alpha Diversity
3.4.7 Beta Diversity
3.4.8 Microbiome-Wide Association Analysis
3.4.9 Community-Level Association Analysis Based on Alpha Diversity
3.4.10 Community-Level Association Analysis Based on Beta Diversity
3.4.11 Biodiversity-Free Test of Microbiome Community Association
3.4.12 Univariate Feature-Wise Associated Analysis Methods
3.4.13 Visualization of Univariate Association Analysis
3.4.14 Machine Learning Methods for Microbial Biomarker Discovery
4 Conclusions
References