RANKS: Ranking of Nodes with Kernelized Score Functions

Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking in biomolecular networks. RANKS can be easily applied to a large set of different relevant problems in computational biology, ranging from automatic protein function prediction, to gene disease prioritization and drug repositioning, and more in general to any bioinformatics problem that can be formalized as a node label ranking problem in a graph. The modular nature of the implementation allows to experiment with different score functions and kernels and to easily compare the results with baseline network-based methods such as label propagation and random walk algorithms, as well as to enlarge the algorithmic scheme by adding novel user-defined score functions and kernels.

Install the latest version of this package by entering the following in R:
install.packages("RANKS")
AuthorGiorgio Valentini -- AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano
Date of publication2015-12-10 10:04:15
MaintainerGiorgio Valentini <valentini@di.unimi.it>
LicenseGPL (>= 2)
Version1.0

View on CRAN

Functions

cauchy.kernel Man page
compute.acc Man page
compute.F Man page
do.GBA Man page
do.loo.RANKS Man page
do.RANKS Man page
do.RW Man page
do.RWR Man page
do.stratified.cv.data Man page
eav.score Man page
eav.score,graph-method Man page
eav.score,matrix-method Man page
eav.score-methods Man page
find.optimal.thresh.cv Man page
gaussian.kernel Man page
GBAmax Man page
GBAsum Man page
identity.kernel Man page
inv.multiquadric.kernel Man page
Kernel functions Man page
ker.score.classifier.cv Man page
ker.score.classifier.holdout Man page
ker.score.cv Man page
KNN.score Man page
KNN.score,graph-method Man page
KNN.score,matrix-method Man page
KNN.score-methods Man page
label.prop Man page
labelsfromscores Man page
laplacian.kernel Man page
linear.kernel Man page
Methods for scoring a single vertex Man page
Methods for scoring multiple vertices Man page
multiple.ker.score.cv Man page
multiple.ker.score.thresh.cv Man page
Multiple.labels.from.scores Man page
multiple.RW.cv Man page
NN.score Man page
NN.score,graph-method Man page
NN.score,matrix-method Man page
NN.score-methods Man page
norm1 Man page
poly.kernel Man page
p.step.rw.kernel Man page
p.step.rw.kernel,graph-method Man page
p.step.rw.kernel,matrix-method Man page
p.step.rw.kernel-methods Man page
RANKS Man page
RANKS-package Man page
RW Man page
RW.cv Man page
rw.kernel Man page
rw.kernel,graph-method Man page
rw.kernel,matrix-method Man page
rw.kernel-methods Man page
RWR Man page
selection.test Man page
single.eav.score Man page
single.eav.score,graph-method Man page
single.eav.score,matrix-method Man page
single.eav.score-methods Man page
single.KNN.score Man page
single.KNN.score,graph-method Man page
single.KNN.score,matrix-method Man page
single.KNN.score-methods Man page
single.NN.score Man page
single.NN.score,graph-method Man page
single.NN.score,matrix-method Man page
single.NN.score-methods Man page
single.WSLD.score Man page
single.WSLD.score,graph-method Man page
single.WSLD.score,matrix-method Man page
single.WSLD.score-methods Man page
Unit.sphere.norm Man page
WSLD.score Man page
WSLD.score,graph-method Man page
WSLD.score,matrix-method Man page
WSLD.score-methods Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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