Fused Sparse Structural Equation Models to Jointly Infer Gene Regulatory Network.
fssemR
fssemR is a package that ultilizes the Proximal Alternating Linearized Maximal to solve the non-convex non-smooth jointly fused sparse structrual equation model.
Installation
fssemR package contains a lot of necessary scripts to analyze large dataset such as microarray and SNP data from GEO database, so it has not been submitted to CRAN yet for these non-standard directory. To install fssemR, you need a C++ compiler such as g++ or clang++ with C++11 feature, and for Windows users, the Rtools software is needed (unless you can configure the toolchain by yourself).
The installation follows the typical way of R packages on Github:
library(devtools)
install_github("Ivis4ml/fssemR")
Now, fssemR package is uploaded on CRAN. So you will install it via CRAN
install.packages("fssemR")
Vignette
Citation
Xin Zhou, Xiaodong Cai, Inference of differential gene regulatory networks based on gene expression and genetic perturbation data, Bioinformatics, , btz529, https://doi.org/10.1093/bioinformatics/btz529
Update
Upgrade to Eigen 0.3.4 compatible.