RANKS: Ranking of Nodes with Kernelized Score Functions

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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.

Author
Giorgio Valentini -- AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano
Date of publication
2015-12-10 10:04:15
Maintainer
Giorgio Valentini <valentini@di.unimi.it>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

do.GBA
GBA cross-validation experiments with multiple classes
do.loo.RANKS
RANKS leave-one-out experiments with multiple classes
do.RANKS
RANKS cross-validation experiments with multiple classes
do.RW
Random walk cross-validation experiments with multiple...
do.RWR
Random walk with restart cross-validation experiments with...
find.optimal.thresh.cv
Function to find the optimal RANKS score thereshold
GBAmax
Guilt By Association (GBA) using the maximum rule
GBAsum
Guilt By Association (GBA) using the sum rule
kernel.functions
Kernel functions
ker.score.classifier.cv
Multiple cross-validation with RANKS for classification
ker.score.classifier.holdout
RANKS held-out procedure for a single class
ker.score.cv
RANKS cross-validation for a single class
label.prop
Label propagation
multiple.ker.score.cv
RANKS multiple cross-validation for a single class
multiple.ker.score.thresh.cv
Function for RANKS multiple cross-validation and optimal...
multiple.RW.cv
Random walk, GBA and labelprop multiple cross-validation for...
RANKS-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("RANKS")}
RW
Random walk on a graph
RW.cv
Random walk, GBA and labelprop cross-validation for a single...
rw.kernel-methods
Random walk kernel
RWR
Random walk with Restart on a graph
score.multiple.vertex-methods
Multiple vertex score functions
score.single.vertex-methods
Single vertex score functions
Utilities
Utility functions

Files in this package

RANKS
RANKS/inst
RANKS/inst/doc
RANKS/inst/doc/index.html
RANKS/inst/doc/RANKS-manual.pdf
RANKS/src
RANKS/src/RANKS.c
RANKS/NAMESPACE
RANKS/R
RANKS/R/RANKS.1.0.R
RANKS/MD5
RANKS/build
RANKS/build/partial.rdb
RANKS/DESCRIPTION
RANKS/man
RANKS/man/multiple.ker.score.cv.Rd
RANKS/man/ker.score.cv.Rd
RANKS/man/find.optimal.thresh.cv.Rd
RANKS/man/do.RANKS.Rd
RANKS/man/RWR.Rd
RANKS/man/multiple.RW.cv.Rd
RANKS/man/ker.score.classifier.cv.Rd
RANKS/man/RANKS-package.Rd
RANKS/man/score.single.vertex-methods.Rd
RANKS/man/RW.cv.Rd
RANKS/man/GBAsum.Rd
RANKS/man/RW.Rd
RANKS/man/do.GBA.Rd
RANKS/man/do.RW.Rd
RANKS/man/ker.score.classifier.holdout.Rd
RANKS/man/Utilities.Rd
RANKS/man/GBAmax.Rd
RANKS/man/rw.kernel-methods.Rd
RANKS/man/score.multiple.vertex-methods.Rd
RANKS/man/do.loo.RANKS.Rd
RANKS/man/label.prop.Rd
RANKS/man/multiple.ker.score.thresh.cv.Rd
RANKS/man/kernel.functions.Rd
RANKS/man/do.RWR.Rd