INSTALL_INSTRUCTIONS.txt

Copyright (c) Nils Blüthgen and Bertram Klinger, 2013-

Gnu General Public Licence

---

The library contains the levmar-package (version 2.5) for optimization (c) by Manolis Lourakis
(see src/levmar-2.5/README.txt)

---

This library can be used to model signalling perturbation data using models that are derived from
Modular Response Analysis, in a way described in Klinger et al, 2013 using R. 

Requires the following C++ libraries to be installed (installation method depends on the OS): 

ginac
cln

And the following R packages: 

Rcpp (>= 0.10.4)
RhpcBLASctl
Rgraphviz
pheatmap
lattice
lhs
parallel

You can install those packages in R with:

source("https://bioconductor.org/biocLite.R")
biocLite(c(“Rccp”,"RhpcBLASctl",”Rgraphviz”,”pheatmap”,"lattice","lhs","parallel"))

Unix (MacOS, BSD, GNU/Linux) installation guide:
For a local installation, first create a folder for local R library in (e.g "home/<Username>/R")
Open shell go to the folder of the package (“MRA_Signaling”)
execute: R CMD INSTALL ./ (when recompiling use R CMD INSTALL --preclean ./)

Have fun with it! 

---

If you use this program in publications, please cite our paper:

Klinger B., Sieber A., Fritsche-Guenther R., Witzel F., Berry L., Schumacher D., Yan Y., Durek P., Merchant M., Schäfer R., Sers C. and Blüthgen N. 
Network quantification of EGFR signaling unveils potential for targeted combination therapy. 
Molecular Systems Biology, 9: 673, 2013