Data Analysis on Metabolomics Data

📖 Procedures

Statistical Analysis

Due to terrible experience on Statistical Analysis in Metabolomics via MetaboAnalystR R package, we try to provide a reproducible and easy-to-use template for visualization, pre-processing, exploration, and statistical analysis on metabolomic data by other packages and scripts. Here, the template comprises the following procedures:

Data Processing
- Data Checking
- Data Filtering
- Missing Value Imputation
- Data Normalization
Cluster Analysis
- Hierarchical Clustering
- Partitional Clustering
Chemometrics Analysis
- Principal Component Analysis (PCA)
- Partial Least Squares-Discriminant Analysis (PLS-DA)
- Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA)
Univariate Analysis
- Fold Change Analysis
- T Tests
- Wilcoxon Test
- Limma Test
- Wilcoxon Test
- Volcano plot
- Correlation Heatmaps
- glasso
Feature selection
- Lasso
- Ridge
- Elasticnet
Classification
- Random Forest
Network Analysis
- SPRING
- Spearman
- SparCC
- Network comparison

Functional Analysis

Following two chapters would focus on the Enrichment Analysis and Pathway Analysis of metabolomic data. Enrichment Analysis includes three sections (i.e., ORA, SSP and QEA) and Pathway Analysis only includes ORA and QEA.

The main difference between Enrichment Analysis and Pathway Analysis are the data set that input metabolites are enriched to. In Enrichment Analysis, input metabolites are enriched to pre-defined metabolite sets while in Pathway Analysis, metabolites are enriched to pathways in KEGG.

Enrichment Analysis
- Single Sample Profiling
- Over representation analysis
- Quantitative Enrichment Analysis
Pathway Analysis
- Over representation analysis
- Quantitative Enrichment Analysis

MetOrigin Analysis

Microbiome and its metabolites are closely associated with human health and diseases. However, it is challenging to understand the complex interplay between microbiome and metabolites. MetOrigin is a bioinformatics tool, aiming to identify which bacteria and how they participate in certain metabolic reactions, helping us to understand where metabolites come from: host, bacteria, or both?

✍️ Authors

Xbiome company

🔧 Change log

Submitted to gitlab. (2022-06-28)
add test.Rmd. (2022-07-05)
add template.Rmd. (2022-07-08)
add README.Rmd. (2022-07-12)
add building bookdwon. (2022-08-04)
add MetOrigin Analysis. (2023-11-22)
update Data Processing. (2023-11-22)
add Tutorial of Function Analysis and MetOrigin Analysis. (2023-11-27)