FELLA: The FELLA package
In b2slab/FELLA: Interpretation and enrichment for metabolomics data

Description Details References Examples

FELLA is a metabolomics data enrichment tool that contextualises a list of metabolites using KEGG reactions, enzymes, modules and pathways [Picart-Armada, 2017].

FELLA can build knowledge models for the desired organism from the KEGG database [Kanehisa, 2017]. Once a model is ready, the input for the enrichment is introduced as a list of affected metabolites (as KEGG IDs). The output contains a comprehensive biological network layout that relates relevant pathways to the affected metabolites. Results are available in network and tabular format.

FELLA is equipped with a simple graphical interface for the lay user, deployed through launchApp.

FELLA relies mainly on the following packages: KEGGREST for the queries to the KEGG server [Tenenbaum, 2013], igraph for the network support [Csardi, 2006] and shiny for the graphical user interface [Chang, 2017].

Methodology:

Picart-Armada, S., Fernandez-Albert, F., Vinaixa, M., Rodriguez, M. A., Aivio, S., Stracker, T. H., Yanes, O., & Perera-Lluna, A. (2017). Null diffusion-based enrichment for metabolomics data. PLOS ONE, 12(12), e0189012.

Database:

Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017). KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic acids research, 45(D1), D353-D361.

Main dependencies:

Tenenbaum, D. (2013). KEGGREST: Client-side REST access to KEGG. R package version, 1(1).

Csardi, G., & Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems, 1695(5), 1-9.

Chang, W., Cheng, J., Allaire, JJ., Xie, Y., & McPherson, J. (2017). shiny: Web Application Framework for R. R package version 1.0.5. https://CRAN.R-project.org/package=shiny

## Walkthrough
browseVignettes("FELLA")
## I: create database
?buildGraphFromKEGGREST
## II: enrich data
?enrich
## III: export results
?exportResults