Package: RANKS 1.1

RANKS: Ranking of Nodes with Kernelized Score Functions

Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking to analyze 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.

Authors:Giorgio Valentini [aut, cre]

RANKS_1.1.tar.gz
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RANKS_1.1.tgz(r-4.4-x86_64)RANKS_1.1.tgz(r-4.4-arm64)RANKS_1.1.tgz(r-4.3-x86_64)RANKS_1.1.tgz(r-4.3-arm64)
RANKS_1.1.tar.gz(r-4.5-noble)RANKS_1.1.tar.gz(r-4.4-noble)
RANKS_1.1.tgz(r-4.4-emscripten)RANKS_1.1.tgz(r-4.3-emscripten)
RANKS.pdf |RANKS.html
RANKS/json (API)

# Install 'RANKS' in R:
install.packages('RANKS', repos = c('https://gvalentini58.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.90 score 7 scripts 212 downloads 8 mentions 51 exports 9 dependencies

Last updated 2 years agofrom:5d89a45f24. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64OKNov 07 2024
R-4.5-linux-x86_64OKNov 07 2024
R-4.4-win-x86_64OKNov 07 2024
R-4.4-mac-x86_64OKNov 07 2024
R-4.4-mac-aarch64OKNov 07 2024
R-4.3-win-x86_64OKNov 07 2024
R-4.3-mac-x86_64OKNov 07 2024
R-4.3-mac-aarch64OKNov 07 2024

Exports:cauchy.kernelcompute.acccompute.Fdo.cv.datado.GBAdo.loo.RANKSdo.RANKSdo.RWdo.RWRdo.stratified.cv.dataeav.scoreeav.w.scorefind.optimal.thresh.cvgaussian.kernelGBAmaxGBAsumidentity.kernelinv.multiquadric.kernelker.score.classifier.cvker.score.classifier.holdoutker.score.cvker.score.holdoutKNN.scoreKNN.w.scorelabel.proplabelsfromscoreslaplacian.kernellinear.kernelmultiple.ker.score.cvmultiple.ker.score.thresh.cvMultiple.labels.from.scoresmultiple.RW.cvNN.scoreNN.w.scorenorm1p.step.rw.kernelpoly.kernelRWRW.cvrw.kernelRWRselection.testsingle.eav.scoresingle.eav.w.scoresingle.KNN.scoresingle.KNN.w.scoresingle.NN.scoresingle.NN.w.scoresingle.WSLD.scoreUnit.sphere.normWSLD.score

Dependencies:BHBiocGenericsgenericsgraphlimmaNetPreProcPerfMeasRBGLstatmod

Readme and manuals

Help Manual

Help pageTopics
RANKS: Ranking of Nodes with Kernelized Score FunctionsRANKS-package RANKS
GBA cross-validation experiments with multiple classesdo.GBA
RANKS leave-one-out experiments with multiple classesdo.loo.RANKS
RANKS cross-validation experiments with multiple classesdo.RANKS
Random walk cross-validation experiments with multiple classesdo.RW
Random walk with restart cross-validation experiments with multiple classesdo.RWR
Function to find the optimal RANKS score theresholdfind.optimal.thresh.cv
Guilt By Association (GBA) using the maximum ruleGBAmax
Guilt By Association (GBA) using the sum ruleGBAsum
Multiple cross-validation with RANKS for classificationker.score.classifier.cv
RANKS held-out procedure for a single classker.score.classifier.holdout ker.score.holdout
RANKS cross-validation for a single classker.score.cv
Kernel functionscauchy.kernel gaussian.kernel identity.kernel inv.multiquadric.kernel Kernel functions laplacian.kernel linear.kernel poly.kernel
Label propagationlabel.prop
RANKS multiple cross-validation for a single classmultiple.ker.score.cv
Function for RANKS multiple cross-validation and optimal threshold finding for a single classmultiple.ker.score.thresh.cv
Random walk, GBA and labelprop multiple cross-validation for a single classmultiple.RW.cv
Random walk on a graphRW
Random walk, GBA and labelprop cross-validation for a single classRW.cv
Random walk kernelp.step.rw.kernel p.step.rw.kernel,graph-method p.step.rw.kernel,matrix-method p.step.rw.kernel-methods rw.kernel rw.kernel,graph-method rw.kernel,matrix-method rw.kernel-methods
Random walk with Restart on a graphRWR
Multiple vertex score functionseav.score eav.score,graph-method eav.score,matrix-method eav.score-methods KNN.score KNN.score,graph-method KNN.score,matrix-method KNN.score-methods Methods for scoring multiple vertices NN.score NN.score,graph-method NN.score,matrix-method NN.score-methods WSLD.score WSLD.score,graph-method WSLD.score,matrix-method WSLD.score-methods
Single vertex score functionsMethods for scoring a single vertex single.eav.score single.eav.score,graph-method single.eav.score,matrix-method single.eav.score-methods single.KNN.score single.KNN.score,graph-method single.KNN.score,matrix-method single.KNN.score-methods single.NN.score single.NN.score,graph-method single.NN.score,matrix-method single.NN.score-methods single.WSLD.score single.WSLD.score,graph-method single.WSLD.score,matrix-method single.WSLD.score-methods
Utility functionscompute.acc compute.F do.cv.data do.stratified.cv.data labelsfromscores Multiple.labels.from.scores norm1 selection.test Unit.sphere.norm
Multiple vertex score functions - weighted versioneav.w.score eav.w.score,graph-method eav.w.score,matrix-method eav.w.score-methods KNN.w.score KNN.w.score,graph-method KNN.w.score,matrix-method KNN.w.score-methods Methods for scoring multiple vertices - weighted version NN.w.score NN.w.score,graph-method NN.w.score,matrix-method NN.w.score-methods
Single vertex score functions - weighted versionMethods for scoring a single vertex - weighted version single.eav.w.score single.eav.w.score,graph-method single.eav.w.score,matrix-method single.eav.w.score-methods single.KNN.w.score single.KNN.w.score,graph-method single.KNN.w.score,matrix-method single.KNN.w.score-methods single.NN.w.score single.NN.w.score,graph-method single.NN.w.score,matrix-method single.NN.w.score-methods