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Differential Abundance Analysis of Microbiome Data
Differential abundance analysis (DDA) is an active area in microbiome research. The main goal of DDA is to identify features (i.e., OTUs, ASVs, taxa,...
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Compositional Analysis of Microbiome Data
This chapter focuses on compositional data analysis (CoDA). First, it describes overall compositional data, the rationale that microbiome data can be...
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Full Shotgun DNA Metagenomics
Full DNA metagenomics is the sequencing of all DNA from a sample followed by assembly and annotation and assignment of sequence information to...
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Databases and Protein Structures
Bioinformatics databases contain biological data from scientific experiments, most importantly DNA and protein sequences and protein structures....
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Multivariate Longitudinal Microbiome Models
Chapter 15 mainly introduced the glmmTMB, GLMMadaptive, and FZINBMM packages. However, all these three packages...
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Alpha Diversity
Population diversity is one important characteristic of a microbiome community, which is highly related to its environment. The change of diversity...
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Basic Data Processing in QIIME 2
This chapter presents some basic data processing in QIIME 2. First it introduces importing and exporting data. Then it introduces extracting data...
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Clustering Sequences into OTUs
This chapter describes and illustrates taxonomic classification of the representative sequences and clustering of OTUs. First it introduces some...
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Sequenced-Based Ty** and Prediction of Function
The population genetic mechanisms responsible for the formation and conservation of populations are introduced. Multilocus sequence ty** is used to...
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DNA Sequence Assembly and Annotation of Genes
This chapter describes the different sequencing strategies, the pros and cons of the different strategies to help you select the optimal DNA...
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Pairwise Alignment, Multiple Alignment, and BLAST
Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or...
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Transcriptomics
The RNA-sequencing (RNA-Seq) method is a relative abundance measurement technology. The primary goal of the differential gene expression analysis is...
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16S rRNA Amplicon Sequencing
The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The...
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Introduction to Phylogenetic Analysis of Molecular Sequence Data
Phylogeny is a model of the relationships between organisms, genes, proteins, or other structures based on common ancestry. It is also used for...
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Zero-Inflated Beta Models for Microbiome Data
This chapter introduces two specifically designed zero-inflated beta regression models for analyzing zero-inflated count microbiome data. First, it...
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Assigning Taxonomy, Building Phylogenetic Tree
Taxonomic classification of the representative sequences and clustering of OTUs (Operational Taxonomic Units) are two core steps in bioinformatic...
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Introduction to R for Microbiome Data
This chapter first introduces some useful R functions and R packages for microbiome data. Then it illustrates some specifically designed R packages...
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Moving Beyond OTU Methods
This chapter investigates the movement of moving beyond OTU methods and discusses the necessity and possibility of this movement. First, it describes...
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Future Prospects of Insect Biotechnology
This chapter emphasizes on future trends of insect biotechnology in protein vaccines production, future crop protection, pest management approaches,...
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Insect Metagenomics
Through this chapter, you will come to know about insect gut metagenomics and how it is helpful for the insect to flourish whatever the condition may...