Dynamic Deterministic Effects Propagation Networks: Infer
signalling networks for timecourse RPPA data.
DDEPN (Dynamic Deterministic Effects Propagation
Networks): Infer signalling networks for timecourse data. Given
a matrix of high-throughput genomic or proteomic timecourse
data, generated after external perturbation of the biological
system, DDEPN models the time-dependent propagation of active
and passive states depending on a network structure. Optimal
network structures given the experimental data are
reconstructed. Two network inference algorithms can be used:
inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA,
a Genetic Algorithm network optimisation. Inclusion of prior
biological knowledge can be done using different network prior
models.

R (>= 2.10.0), graph (>= 1.20), Rgraphviz (>= 1.21.3),
KEGGgraph (>= 1.1.0), RBGL, genefilter, gam, lattice, coda

R (>= 2.10.0), graph (>= 1.20), Rgraphviz (>= 1.21.3),
KEGGgraph (>= 1.1.0), RBGL, genefilter, gam, lattice, coda,
gplots

R (>= 2.10.0), genefilter, gam, lattice, coda, gplots, graph,
igraph0, RBGL, cluster

R (>= 2.14), genefilter, gam, lattice, coda, gplots, graph,
igraph0, RBGL, cluster

R (>= 2.10.0), genefilter, gam, lattice, coda, gplots, graph,
igraph, RBGL

R (>= 2.14), lattice, coda, igraph, graph
DDEPN (Dynamic Deterministic Effects Propagation Networks): Infer signalling networks for timecourse data. Given a matrix of high-throughput genomic or proteomic timecourse data, generated after external perturbation of the biological system, DDEPN models the time-dependent propagation of active and passive states depending on a network structure. Optimal network structures given the experimental data are reconstructed. Two network inference algorithms can be used: inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA, a Genetic Algorithm network optimisation. Inclusion of prior biological knowledge can be done using different network prior models.

Alex Couture-Beil <alex@mofo.ca>,
Jon T. Schnute <SchnuteJ@pac.dfo-mpo.gc.ca>, and
Rowan Haigh <HaighR@pac.dfo-mpo.gc.ca>
This package solves systems of delay differential equations.
by interfacing numerical routines written by Simon N. Wood.
These numerical routines first appeared in Simon Wood's solv95 program.