...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
This will also install all required dependencies and you are good to go :)
You can start using the package by importing it:
Documentation can be found using the included help in R (
instance). An example using the Human Red Blood Cell model can be found in the
package 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.
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