DrugClust: Implementation of a Machine Learning Framework for Predicting Drugs Side Effects

An implementation of a Machine Learning Framework for prediction of new drugs Side Effects. Firstly drugs are clustered with respect to their features description and secondly predictions are made, according to Bayesian scores. Moreover it can perform protein enrichment considering the proteins clustered together in the first step of the algorithm. This last tool is of extreme interest for biologist and drug discovery purposes, given the fact that it can be used either as a validation of the clusters obtained, as well as for the possible discovery of new interactions between certain side effects and non targeted pathways. Clustering of the drugs in the feature space can be done using K-Means, PAM or K-Seeds (a novel clustering algorithm proposed by the author).

Author
Giovanna Maria Dimitri
Date of publication
2016-04-23 14:19:13
Maintainer
Giovanna Maria Dimitri <gmd43@cam.ac.uk>
License
GPL-2
Version
0.2

View on CRAN

Man pages

AUC
AUC
AUPR
AUPR
CreateFolds
CreateFolds
DrugClustKMeans
DrugClustKMeans
DrugClustKMeansEnrichment
DrugClustKMeansEnrichment
DrugClustKSeeds
DrugClustKSeeds
DrugClustKSeedsEnrichment
DrugClustKSeedsEnrichment
DrugClustPAM
DrugClustPAM
DrugClustPAMEnrichment
DrugClustPAMEnrichment
Enrichment_Proteins
Enrichment_Proteins
InitFeatures
InitFeatures
InitSideEffect
InitSideEffect
KMeansClusteringAlgorithm
KMeans
KMeansModel
KMeansModel
KSeedsClusters
KSeedsClusters
KSeedsScores
KSeedsScores
PAM
PAM
PAM_Model
PAM_Model
PredictionKMeans
PredictionKMeans
PredictionKSeeds
PredictionKSeeds
Prediction_PAM
Prediction_PAM
RandomSeedGenerator
RandomSeedGenerator
SeedSelection
SeedSelection

Files in this package

DrugClust
DrugClust/NAMESPACE
DrugClust/R
DrugClust/R/DrugClustKSeeds.R
DrugClust/R/VariousFunctions.R
DrugClust/R/SampleScriptsCommands.R
DrugClust/R/enrichmentGO.R
DrugClust/R/DrugClustKMeans.R
DrugClust/R/DrugClustPAM.R
DrugClust/MD5
DrugClust/DESCRIPTION
DrugClust/man
DrugClust/man/DrugClustPAM.Rd
DrugClust/man/AUPR.Rd
DrugClust/man/RandomSeedGenerator.Rd
DrugClust/man/PredictionKSeeds.Rd
DrugClust/man/AUC.Rd
DrugClust/man/DrugClustKMeansEnrichment.Rd
DrugClust/man/InitSideEffect.Rd
DrugClust/man/DrugClustKSeeds.Rd
DrugClust/man/DrugClustKSeedsEnrichment.Rd
DrugClust/man/DrugClustKMeans.Rd
DrugClust/man/KMeansClusteringAlgorithm.Rd
DrugClust/man/KSeedsClusters.Rd
DrugClust/man/DrugClustPAMEnrichment.Rd
DrugClust/man/InitFeatures.Rd
DrugClust/man/Prediction_PAM.Rd
DrugClust/man/CreateFolds.Rd
DrugClust/man/PredictionKMeans.Rd
DrugClust/man/Enrichment_Proteins.Rd
DrugClust/man/PAM_Model.Rd
DrugClust/man/SeedSelection.Rd
DrugClust/man/KMeansModel.Rd
DrugClust/man/KSeedsScores.Rd
DrugClust/man/PAM.Rd