Welcome! the idea of this tutorial is to give you basic statistical and visualization tools by reproducing the analysis of this paper:
Impact of Dietary Interventions on Pre-diabetic Oral and Gut Microbiome, Metabolites and Cytokines
Shoer et al. Nature Communications, 2023. https://doi.org/10.1038/s41467-023-41042-x
The paper describes a clinical study that asks: What is the impact of the two dietary interventions on thousands of measurements?
The biological goal is to gain insights into the changes induced by the interventions and identify potential therapeutic targets for managing hyperglycemia and associated comorbidities.
By solving this tutorial you will gain the following computational tools and skills:
- Data processing techniques to handle tabular data
(juyter notebook, pandas and numpy packages) - Visualization techniques to effectively communicate results
(matplotlib, seabron, plotly and statannot packages) - Statistical tests for comparative analysis and hypothesis testing
(parametric vs non-parametric test, paired vs unpaired test, multiple hypothesis correction, bootstrap) - Mediation analysis to explore potential causal relationships
(linear models, covariates, a bit of causality) - Model evaluation on a validation set
(correlation, coefficent of determination and explained variance) - Sensitivity to sample size and the law of small numbers
Good luck!