RANKS: a flexible tool for node label ranking and classification in biological networks
Summary: 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.
Source: Bioinformatics - Category: Bioinformatics Authors: Valentini, G., Armano, G., Frasca, M., Lin, J., Mesiti, M., Re, M. Tags: SYSTEMS BIOLOGY Source Type: research