Data containers are in core

SummarizedExperiment

(Huber et al. 2015)

SummarizedExperiment class

TreeSummarizedExperiment

(Huang et al. 2021)

TreeSummarizedExperiment class

Orchestrating Microbiome Analysis, OMA

  • Microbiome data science ecosystem
  • Packages (mia top 8.05% in Bioconductor)
  • Bioconductor book

Bioconductor sticker mia logo

Building the microbiome community in Bioconductor

  • Common data standard TreeSummarizedExperiment
  • Interoperable software (methods from international community)
  • Shared knowledge (online book)
  • Open collaboration

Thank you for your time!

Orchestrating Microbiome Analysis online book

References

https://microbiome.github.io/

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.