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 7.8% 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

Poem of the day

Put it in the book, make it clear,
mia framework’s waiting here.

OMA’s guide will light the way,
helping you every step of the day.

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.