retnfit

Fitting ternary network models of gene regulatory networks by replica exchange Monte Carlo

H. R. McMurray, A. Ambeskovic, L.A. Newman, J. Aldersley, V. Balakrishnan, B. Smith, H. A. Stern, H. Land, and M. N. McCall, "Gene network modeling via TopNet reveals functional dependencies between diverse tumor-critical mediator genes," Cell Reports 37, 110136 (2021) doi.org/10.1016/j.celrep.2021.110136
H. R. McMurray, H. A. Stern, A. Ambeskovic, H. Land, and M. N. McCall, “Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments,” STAR protocols 3, 101737 (2022) doi.org/10.1016/j.xpro.2022.101737

To install parallel (openMP and MPI) version, run

autoconf

in retnfit directory before

R CMD build retnfit

For MPI version, run

R CMD INSTALL --clean retnfit_0.99.17.tar.gz --configure-args='--with-mpi=/path/to/mpi-1.x  --with-Rmpi-type=OPENMPI'

For CUDA version

Update the driver.c file with the experiment data

Go to cuda/ and run make

This generates an executable driver

To run : ./driver