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

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

Use limitation: MIT

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
)

Operation name: Analysis of microbial profiles

Description: A set of R scripts for the analysis of microbial profiles

Function: A set of R scripts for the analysis of microbial profiles

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

Metadata

File identifier: 57a42fde-aa63-4982-a7b7-05daed8a7e55 XML

Metadata language: en

Hierarchy level: Service

Metadata Schema Version: 1.0

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