Software & Tools
- GBM-cRegMap (web server): A co-regulatory influence map of glioblastoma heterogeneity and evolution – From cells in vitro to tumors and back again.
- BLCA-cRegMap (web server): A co-regulatory influence map of bladder cancer heterogeneity and evolution – From cells in vitro to tumors and back again.
- BRCA-cRegMap (web server): A co-regulatory influence map of breast cancer heterogeneity and evolution – From cells in vitro to tumors and back again.
- PDAC-cRegMap (web server): A co-regulatory influence map of pancreatic cancer heterogeneity and evolution – From cells in vitro to tumors and back again.
- H-Licorn: learning cooperative gene regulatory networks from transcriptome data
- CoRegNet: is an R bioconductor package, which enables infers master regulators controlling the transition between phenotypes.
- CoRegFlux: R Bioconductor package. Integrating transcriptional activity in genome-scale models of metabolism.
- LatNet: R package. Latent network-based representations for large-scale gene expression data analysis.
- PEPPER: is a plugin cytoscape, which enables finding pathways connecting a protein set within a PPI-network using multi-objective optimization.
- WRFO (python package) : Weighted Random Forest Optimization
- GLOW (python package): Learning Global-Local Multi-Scale Node Embeddings with Random Walks and Landmark-Guided Optimization
- SkyClust (Java): Clustering attributed graph using multi-objective optimization.