Rhea: R scripts for the analysis of microbial profiles | Marinevre

Rhea: R scripts for the analysis of microbial profiles

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs.

The Rhea pipeline is a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalisation steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be used as a framework for advanced users who can modify and expand the tool.

Rhea is composed of 6 steps that can be run independently or as a set.

  • Normalization
  • Alpha-Diversity
  • Beta-Diversity
  • Taxonomic-Binning
  • Serial-Group-Comparisons
  • Correlations

These scripts can be downloaded from its website , and you can also go directtly to its GitHub repository


Developed by: 
Ilias Lagkouvardos, IMBCC-HCMR
Used data resources: 
User OTU table, user metadata
Technology or platform: