Microbiome data science

  • Interactions between microbes and host
  • Sequencing data - Other omics regularly incorporated
Moreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.
(Moreno-Indias et al. 2021)

Challenges

Lack of…

  • Standardization
  • Scalability, support for multi-table data
  • Interoperability with other fields
Moreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.
(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)