retnfit

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

references:

• 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