| GRAPE | Rust/Python Graph Representation Learning library for Prediction and Evaluation | 
| parSMURF | A High-performance Computing tool to detect pathogenic variants in the human genome | 
| HyperSMURF | Machine learning supervised method to learn rare pathogenic variants in imbalanced genomic data sets | 
| HEMDAG | An R software library implementing Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs | 
| obogaf::parser | A perl5 module to handle obo and gaf file | 
| COSNet | Neural network algorithm for semi-supervised node label learning from unbalanced data | 
| UNIPred | Unbalance-aware Network Integration and Prediction of protein functions | 
| HCGene | R package to support the hierarchical classification of genes | 
| Clusterv | R package for cluster validation | 
| Mosclust | R package for the discovery of significant structures in bio-molecular data | 
| NEURObjects | Set of C++ library classes for neural networks development | 
| PerfMeas | R package implementing different performance measure for classification and ranking tasks | 
| NetPreProc | R package that implements preprocessing and normalization methods for network-structured data | 
| Bionetdata | R data package that includes several examples of chemical and biological data networks |