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Bioinformatics. 2016 Sep 15;32(18):2872-4. doi: 10.1093/bioinformatics/btw235. Epub 2016 Jun 2.

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

Author information

1
AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
2
Department of Electric and Electronic Engineering, University of Cagliari, 09123 Cagliari, Italy.

Abstract

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.

PMID:
27256314
DOI:
10.1093/bioinformatics/btw235
[Indexed for MEDLINE]
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