FUNctional toolKIt platform for multi-omic functional analysis. An standardised pipeline to analysis transcriptomic, proteomic, phosphoproteomic and metabolomic datasets.


FUNKI is accessible on shinyapps or to run locally.

| :warning: | Online version does NOT support CARNIVAL/COSMOS to be run with cplex or cbc. This software is licenced-based, so the LOCAL version of FUNKI is advided (previous installation of the selected software) | |—————|:————————|

To run FUNKI locally, there are different options to fit all possible users:

  1. Run FUNKI directly from GitHub

In an R session, run the line below to launch FUNKI:

shiny::runGitHub(repo = "ShinyFUNKI", username = "saezlab", subdir = "FUNKI")

| :point_up: | Remember to have all required packages installed beforehand! | |—————|:————————|

The renv.lock lockfile (renv packaged) has recorded the state of this project’s private library. It can be used to restore the state of that library as required by calling renv::restore().

  1. Download the repository and run FUNKI

In an R session, run the line below to launch FUNKI once this repo has been downloaded/cloned:


As in case 1, all required packages must be installed beforehand. The renv.lock lockfile can be used to resore the library by calling renv::restore().

  1. Create a docker for FUNKI

The docker file is provided to create a docker imagine.

To build the docker image:

This process takes some time (~ 2400s).

To create a container just run:

And there it is, running on localhost:3838

| :point_up: | Remember to install cplex or cbc to use CARNIVAL/COSMOS with these softwares! | |—————|:————————|