MIGRATED: This repository has moved

Hi! This repository is no longer active on GitHub.

Our research group (b2slab) has moved away from GitHub as part of our commitment to EU data sovereignty (keeping our development tooling and data under infrastructure and governance that better aligns with European requirements and values).

The active repository is now hosted on Forgejo here: https://dev.b2s.club/b2slab/FELLA

If you landed here from an old link, please update your remotes and bookmarks. Thanks!

Enriching metabolomics data through diffusion

This repository contains the FELLA package. FELLA is a metabolomics data enrichment tool that contextualises the experimental results using KEGG reactions, enzymes, modules and pathways.

• The input for our package is a list of affected metabolites between experimental conditions.
• The layout of the analysis is in a comprehensive human-readable layout, exportable to several formats, containing a biological interpetation of the experiment.

The subnetwork displayed to the user is found using diffusive processes on a graph that represents the known biological annotations at several molecular levels. To use this package type in your terminal:

R CMD build FELLA
R CMD INSTALL FELLA

Alternatively, you can use devtools if you experience some trouble building the vignette. Working in the package directory, this should do the trick:

devtools::install(build_vignettes = T)

Once FELLA is installed, you may load it by typing in your R terminal

library("FELLA")

To get the global picture about FELLA usage, you may browse its vignette

browseVignettes("FELLA")

All of the functions in FELLA have a (very basic) documentation, inclusive the package and the sample data FELLA.sample and input.sample.

In addition, there is a shiny app to facilitate the usage of the package. Before launching it, a database should be built. For example, for Homo sapiens excluding the hsa01100 pathway:

g <- buildGraphFromKEGGREST(
  organism = "hsa", 
  filter.path = "hsa01100"
)
buildDataFromGraph(g)

Then we can launch the shiny app

FELLA:::launchApp(
  host = "127.0.0.1", 
  port = 8888
)

and leave the command active. Going to the direction http://127.0.0.1:8888 will start the analysis.