Orchestrating Microbiome Analysis with Bioconductor

Tuomas Borman

Microbiome data science

• Interactions between microbes and host
• Sequencing data - Other omics regularly incorporated

(Moreno-Indias et al. 2021)

Challenges

Lack of…

• Standardization
• Scalability, support for multi-table data
• Interoperability with other fields

(Moreno-Indias et al. 2021)

Data containers

• The core of software
• Structured, standardized way to manage complex data
• Enables modular, efficient workflows

SummarizedExperiment

(Huber et al. 2015)

TreeSummarizedExperiment

(Huang et al. 2021)

Microbiome Analysis (mia)

• Microbiome data science in SummarizedExperiment ecosystem
• Distributed through several R packages
• mia package top 8.2% 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

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

Interoperable with the SummarizedExperiment ecosystem

Online book

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

Acknowledgements

Leo Lahti, Felix M. Ernst, Giulio Benedetti, Sudarshan Shetty, Muluh Geraldson, Akewak Jeba, Thomaz Bastiaanssen, Aura Raulo, Levi Waldron, Henrik Eckermann, Chouaib Benchraka, Yağmur Şimşek, Basil Courbayre, Matti Ruuskanen, Stefanie Peschel, Christian L. Müller, Aki Havulinna, Shigdel Rajesh, Artur Sannikov, Himmi Lindgren, Lu Yang, Katariina Pärnänen, Noah de Gunst, Axel Dagnaud, Ely Seraidarian, Théotime Pralas, Jiya Chaudhary, Elina Chiesa, Pande Erawijantari, Shadman Ishraq, Sam Hillman, Matteo Calgaro, Basil Courbayre Dussau, Yang Cao, Eineje Ameh, Domenick J. Braccia, Renuka Potbhare, Hervé Pagès, Moritz E. Beber, Vivian Ikeh, Yu Gao, Daniel Garza, Karoline Faust, Jacques Serizay, Himel Mallick, Yihan Liu, Danielle Callan, Ben Allen, Teo Dallier, Elliot Gaudron-Parry, Inès Benseddik, Jesse Pasanen, Benjamin Valderrama

Thank you for your time!

Orchestrating Microbiome Analysis online book

References

Huang, Ruizhu, Charlotte Soneson, Felix G. M. Ernst, et al. 2021. “TreeSummarizedExperiment: A S4 Class for Data with Hierarchical Structure.” F1000Research 9: 1246. https://doi.org/10.12688/f1000research.26669.2.

Huber, W., V. J. Carey, R. Gentleman, S. Anders, M. Carlson, B. S. Carvalho, H. C. Bravo, et al. 2015. “Orchestrating High-Throughput Genomic Analysis with Bioconductor.” Nature Methods 12 (2): 115–21. http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html.

Moreno-Indias, Isabel, Leo Lahti, Miroslava Nedyalkova, Ilze Elbere, Gennady V. Roshchupkin, Muhamed Adilovic, Onder Aydemir, et al. 2021. “Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.” Frontiers in Microbiology 12: 277. https://doi.org/10.3389/fmicb.2021.635781.