Software

MUMI: Multitask module identification for biological networks

Weiqi Chen developed an algorithm called MUMI (MUltitask Module Identification) to detect the overlaps between active modules and communities simultaneously. The MATLAB source code is available at Github.

AMOUNTAIN: Active modules for multilayer weighted gene co-expression networks

Dong Li developed a novel algorithm to identify active modules from multilayer weighted gene co-expression networks based on a convex optimization approach. You can download the source code from our Github or the R package from the R Bioconductor page

ATEN: And/Or Tree Ensemble for inferring accurate Boolean network topology and dynamics

Ning developed a Boolean network inference algorithm based on And/Or tree ensemble to accurate Boolean network topology and dynamics from short and noisy time series data. The R package is available at Github

MODA: Module differential analysis for weighted gene co-expression network

Dong Li developed a R package to conduct module differential analysis for weighted gene co-expression networks based on WGCNA, a popular algorithm for weighted co-expression network analysis. You can download the source code from Github.

DiME: A Scalable Disease Module Extraction Algorithm

Yunpeng Liu developed a disease module extracted algorithm for biological networks. We have applied the algorithm to Glioma progression gene expression dataset and discovered several new potential regulators. The paper was published in PLOS ONE. You can download the source code and R package from the software webpage, where you can also find a comprehensive user guide and a sample dataset.