Computational biology software tools

We designed and implemented several open source R libraries, available on-line, to analyze and process complex bio-molecular data:

HCGene an R package to support the hierarchical classification of genes (Valentini and Cesa-Bianchi, 2008)
Clusterv an R package for cluster validation (Valentini, 2006)

Mosclust an R package for the discovery of significant structures in bio-molecular data (Valentini, 2007)

The following R packages are downloadable from the CRAN website:

PerfMeas an R package implementing different performance measure for classification and ranking tasks (v. 1.1)
NetPreProc an R package that implements preprocessing and normalization methods for network-structured data (v. 1.0)
Bionetdata an R data package that includes several examples of chemical and biological data networks (v. 1.0)

We contributed also to the development of GOSSTO, a software tool for the computation of the semantic similarity between GO terms and between genes, in collaboration with the PaccanaroLab, Department of Computer Science, Royal Holloway, University of London (Caniza et al. 2013, Caniza et al. 2014)

Publications

H. Caniza, A. Romero, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, A. Paccanaro, GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology, Bioinformatics, 2014 (accepted for publication)

H. Caniza, A. E. Romero, S. Heron, H. Yang, M. Frasca, M. Mesiti, G. Valentini and A. Paccanaro GOssTo & GOssToWeb: user-friendly tools for calculating semantic similarities on the Gene Ontology, Bio-Ontologies SIG 2013 ISMB 2013, Berlin

Bioinformatics, 24(5), pp. 729-731, 2008.