Rhea: R scripts for the analysis of microbial profiles

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

Default

Date ( Publication)
2019-08-14
Status
Completed
Point of contact
  IMBCC-HCMR - Ilias Lagkouvardos

Keywords

data management
Keywords

metagenomics
Keywords

taxonomy
Keywords

rRNA
Keywords

ASSEMBLE Plus
Keywords

R package
Keywords

calculation tool
Keywords

bioinformatics
Access constraints
License
Other constraints

https://github.com/Lagkouvardos/Rhea/blob/master/LICENSE

OnLine resource
Rhea Web address (

WWW:LINK-1.0-http--link

 )
OnLine resource
Rhea Code repository (

WWW:LINK-1.0-http--link

 )
Topic Category
Species distribution
Service Category

data processing
Service Category

data analysis
Service Language
eng
Service TRL
TRL 9 – Actual system proven in operational environment

metadataMetadata

File identifier
57a42fde-aa63-4982-a7b7-05daed8a7e55 XML
Metadata language
en
Hierarchy level
Service
Metadata Schema Version

1.0
 
 

Overviews

overview
metagenomics.jpg

Spatial extent

Keywords



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