Quarto Presentations

Overview

This website hosts quarto presentations about microbiome analysis and data integration with mia and other related packages. Our presentations were prepared for past courses and conferences and cover a broad range of topics in the scope of biological data science. Currently, you can find the following subjects:

Bioconductor

• Intro
• Bioconductor project
• Orchestrating Microbiome Analysis with Bioconductor

Quarto

• Reproducible workflow with Quarto
• Learning environment
• Workflow

Packages

• MGnifyR: An R package for accessing MGnify microbiome data

Data containers

• Orchestrating microbiome multi-omics with R & Bioconductor
• Data containers
• SummarizedExperiment
• TreeSummarizedExperiment

Example data

• HintikkaXOData
• Tengeler2020

Microbiome data analysis

• Data Manipulation
• Introduction to Quarto
• Alpha Diversity
• Ordination
• Compositional Heatmaps
• Differential Abundance
• Day 2

Contributions

You are welcome to add new presentations or improve the current ones. The guidelines for contributors are explained here. The presentations are deployed from the quarto sub-directory, so you need to make the respective changes there and run cd quarto/; quarto render.

The following is a quick workflow for contributions:

1. fork the repository

2. add your qmd file(s) to the quarto sub-directory

3. update the _quarto.yml file and the list of presentations in the website with the name of the qmd file(s) with your presentation(s)

4. run quarto render, or in R quarto::quarto_render(myfilename) from your terminal from within the quarto sub-directory

5. and make a pull request to the master branch

This documentation provides more details about publishing quarto presentations with GitHub Pages.