RANKS: a flexible tool for node label ranking and classification in biological networks.

ABSTRACT

UNLABELLED RANKS is a flexible software package that can be easily applied to any bioinformatics task formalizable as ranking of nodes with respect to a property given as a label, such as automated protein function prediction, gene disease prioritization and drug repositioning. To this end RANKS provides an efficient and easy-to-use implementation of kernelized score functions, a semi-supervised algorithmic scheme embedding both local and global learning strategies for the analysis of biomolecular networks. To facilitate comparative assessment, baseline network-based methods, e.g. label propagation and random walk algorithms, have also been implemented. AVAILABILITY AND IMPLEMENTATION The package is available from CRAN https//cran.r-project.org/ The package is written in R, except for the most computationally intensive functionalities which are implemented in C. CONTACT valentini@di.unimi.it SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.