Rhea is a bioinformatic pipeline written in

R language R, or r, is the eighteenth letter of the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is ''ar'' (pronounced ), plural ''ars''. The lette ...

for the analysis of microbial profiles. It was released during the end of 2016 and it is publicly available through a

GitHub GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...

repository. Starting with an

Operational taxonomic unit An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, wh ...

(OTU) table, the pipeline contains scripts that perform the following common analytical steps: # Normalization of the OTU table # Calculation of the

alpha diversity In ecology, alpha diversity (α-diversity) is the mean species diversity in a site at a local scale. The term was introduced by R. H. WhittakerWhittaker, R. H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monogra ...

for each sample # Calculation of

beta diversity In ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity. The term was introduced by Robert Whittaker (ecologist), R. H. Whittaker together with the terms alpha diversity (α-diversi ...

and visualization of the results with PCoA # Taxonomic binning # Statistical testing # Correlation analysis The name Rhea was primarily given to the pipeline as a phonetic and visual link to the R language used throughout development. Moreover, as stated in the original publication, the name was chosen to reflect the flowing and evolving nature of the scripts, as "flow" is one of the suggested etymology of the name of the mythological goddess Rhea.

References

R (programming language) Free R (programming language) software Software using the MIT license Science software for Linux {{science-software-stub