# Enriching metabolomics data through diffusion
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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
To get the global picture about `FELLA` usage, you may browse its __vignette__
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"
Then we can launch the shiny app
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.