Rhea (pipeline)

Rhea

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Rhea

Developer(s)| Ilias Lagkouvardos, Sandra Fischer, Neeraj Kumar, Thomas Clavel
Initial release| 16 November 2016 (2016-11-16)
Stable release|

1.1.0

Written in| R
Operating system| Windows, macOS, Ubuntu, Fedora, Red Hat Linux, openSUSE
License| MIT License
Website| https://lagkouvardos.github.io/Rhea/

Rhea[1] is a bioinformatic pipeline written in R language for the analysis of microbial profiles. It was released during the end of 2016 and it is publicly available through a GitHub repository.[2]

Starting with an Operational taxonomic unit (OTU) table, the pipeline contains scripts that perform the following common analytical steps:

1. Normalization of the OTU table
2. Calculation of the alpha diversity for each sample
3. Calculation of beta diversity and visualization of the results with PCoA
4. Taxonomic binning
5. Statistical testing
6. 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,[1] 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

[edit]

1. ^ a b Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas (11 January 2017). "Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons". PeerJ. 5: e2836. doi:10.7717/peerj.2836. PMC 5234437. PMID 28097056.
2. ^ "Rhea by Lagkouvardos". lagkouvardos.github.io.

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R (programming language)

Features|

* Sweave

Implementations|

* Distributed R
* Microsoft R Open (Revolution R Open)
* Renjin

Packages|

* Bibliometrix
* easystats
* qdap
* lumi
* RGtk2
* Rhea
* Rmetrics
* rnn
* RQDA
* Shiny
* SimpleITK
* Statcheck
* tidyverse
* ggplot2
* dplyr
* knitr

Interfaces|

* Bio7
* Emacs Speaks Statistics
* Java GUI for R
* KH Coder
* Rattle GUI
* R Commander
* RExcel
* RKWard
* RStudio

People|

* Roger Bivand
* Jenny Bryan
* John Chambers
* Peter Dalgaard
* Dirk Eddelbuettel
* Robert Gentleman
* Ross Ihaka
* Thomas Lumley
* Brian D. Ripley
* Julia Silge
* Luke Tierney
* Hadley Wickham
* Yihui Xie

Organisations|

* R Consortium
* Revolution Analytics
* R-Ladies
* Posit PBC (formerly RStudio PBC)

Publications|

* The R Journal

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