title: RANKS: a flexible tool for node label ranking and classification in biological networks.
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.
  
  
  
  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.
  
  
  
  valentini@di.unimi.it
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valentini
authors.affiliation: Department of Electric and Electronic Engineering, University of Cagliari, 09123 Cagliari, Italy.
authors.forename: Giuliano
authors.initials: G
authors.lastname: Armano
authors.affiliation: AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Frasca
authors.affiliation: AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
authors.forename: Jianyi
authors.initials: J
authors.lastname: Lin
authors.affiliation: AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Mesiti
authors.affiliation: AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Re
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D058492:Drug Repositioning; D023281:Genomics; D006801:Humans; D011506:Proteins; D012984:Software; D049490:Systems Biology
chemical_list: D011506:Proteins