Orchestrating Microbiome Analysis with Bioconductor

Outline

Bioconductor

• Community-driven open-source project

1. Training programs & workshops
2. Conferences & community support
3. Bioinformatics software

Software

• ~2,300 R packages
• Review, testing, documentation

Data containers form the core

SummarizedExperiment

• Most common data container
• Optimized for biological data
• Extended to different purposes

Optimal container for microbiome data?

Optimal container for microbiome data?

• Multiple assays: seamless interlinking

Optimal container for microbiome data?

• Multiple assays: seamless interlinking
• Hierarchical data: supporting samples & features

Optimal container for microbiome data?

• Multiple assays: seamless interlinking
• Hierarchical data: supporting samples & features
• Side information: extended capabilities & data types

Optimal container for microbiome data?

• Multiple assays: seamless interlinking
• Hierarchical data: supporting samples & features
• Side information: extended capabilities & data types
• Optimized: for speed & memory

Optimal container for microbiome data?

• Multiple assays: seamless interlinking
• Hierarchical data: supporting samples & features
• Side information: extended capabilities & data types
• Optimized: for speed & memory
• Integrated: with other applications & frameworks

Optimal container for microbiome data?

• Multiple assays: seamless interlinking
• Hierarchical data: supporting samples & features
• Side information: extended capabilities & data types
• Optimized: for speed & memory
• Integrated: with other applications & frameworks

Reduce overlapping efforts, improve interoperability, ensure sustainability.

TreeSummarizedExperiment

• Extension to SummarizedExperiment
• Optimal for microbiome data
• Links microbiome field to larger SummarizedExperiment family

MIcrobiome Analysis (mia)

• Microbiome data science in SummarizedExperiment ecosystem
• Distributed through several R packages
• mia package top 8.1% Bioconductor downloads

Community-driven ecosystem of tools

• mia (Data analysis)
• miaViz (Visualization)
• miaSim (Simulation)
• miaTime (Time series analysis)
• miaDash (Graphical user interface)
• iSEEtree (Interactive visualization)
• Expanded by independent developers

Advantages

• Shared data container
• Scalable & optimized for large datasets
• Comprehensive documentation

Allows us to develop efficient microbiome data science workflows

Orchestrating Microbiome Analysis with Bioconductor

• Resources and tutorials for microbiome analysis
• Community-built best practices
• Open to contributions!

Go to the Orchestrating Microbiome Analysis (OMA) online book

microbiome.github.io/OMA

Thank you for your time!

Moreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.