cdiener / dycone Goto Github PK

...analyze enzyme regulation with metabolome data

Dycone ("dynamic cone") allows you infer enzymatic regulation from metabolome mesurements. It employs formalisms based on flux and k-cone analysis to connect metabolome data to distinct regulations of enzyme activity. Most of the analysis methods can be applied to genome-scale data.

If you use dycone in your academic work you may use the following paper for a citation

Diener C, Muñoz-Gonzalez F, Encarnación S, Resendis-Antonio O.
The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome.
Sci Rep. 2016 Jun 23;6:28415. doi: 10.1038/srep28415. PubMed PMID: 27335086.

Even though dycone can be installed directly via R as described in the following section, some of its dependencies require the installation of packages via your package manager. Under Debian and Ubuntu you can install those dependencies via

sudo apt-get install libcurl4-openssl-dev libssl-dev libgmp-dev

In case you do not have R installed you will also need to install it via

sudo apt-get install r-base r-base-dev

The package can be installed directly from github by using devtools:

install.packages("devtools")
devtools::install_github("cdiener/dycone")

This will also install all required dependencies and you are good to go :)

You can start using the package by importing it:

library(dycone)

Documentation can be found using the included help in R (?function_name for instance). An example using the Human Red Blood Cell model can be found in the package vignette "eryth":

vignette("eryth")

For an exhaustive example you can look at the Rmarkdown generated protocol at https://github.com/cdiener/kcone-paper.

To see planned changes to dycone please consult the project milestones.