Rhea
is a
bioinformatic pipeline
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...
written in
R language
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinforma ...
for the analysis of microbial profiles. It was released during the end of 2016 and it is publicly available through a
GitHub repository.
Starting with an
Operational taxonomic unit (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 Monograp ...
for each sample
# Calculation of
beta diversity
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiod ...
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
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