SVM2CRM: SVM2CRM: support vector machine for cis-regulatory elements detections

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Detection of cis-regulatory elements using svm implemented in LiblineaR.

Author
Guidantonio Malagoli Tagliazucchi <malagoli@ingm.org>
Date of publication
None
Maintainer
Guidantonio Malagoli Tagliazucchi <guidantonio.malagolitagliazucchi@unimore.it>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

cisREfindbed
Create and preprocessing of the input for SVM2CRM analysis
createBed
Create bed file of predictions using svm.
createSVMinput
Take the output of findFeatureOverlap and then create a...
featSelectionWithKmeans
This function select the most meaningful variables in a...
findFeatureOverlap
Find the overlap of genomic regions between the output of...
frequencyHM
frequencyHM
getSignal
Model the signals of each histone marks around genomic...
performanceSVM
Estimate the performance of prediction.
plotFscore
Plot the F-score in relation with the sensitivity and...
plotROC
Plot the ROC curve of the best model
predictionGW
Perform prediction of cis-regulatory elements genome-wide
smoothInputFS
Smooth the signals of the histone marks to prepare the input...
tuningParametersCombROC
Test different models using different kernel of SVM, values...

Files in this package

SVM2CRM/DESCRIPTION
SVM2CRM/NAMESPACE
SVM2CRM/NEWS
SVM2CRM/R
SVM2CRM/R/cisREfindbed.R
SVM2CRM/R/createBed.R
SVM2CRM/R/createSVMinput.R
SVM2CRM/R/featSelectionWithKmeans.R
SVM2CRM/R/findFeatureOverlap.R
SVM2CRM/R/frequencyHM.R
SVM2CRM/R/getSignal.R
SVM2CRM/R/performanceSVM.R
SVM2CRM/R/plotFscore.R
SVM2CRM/R/plotROC.R
SVM2CRM/R/predictionGW.R
SVM2CRM/R/smoothInputFS.R
SVM2CRM/R/tuningParametersCombROC.R
SVM2CRM/README
SVM2CRM/build
SVM2CRM/build/vignette.rds
SVM2CRM/inst
SVM2CRM/inst/doc
SVM2CRM/inst/doc/SVM2CRM.R
SVM2CRM/inst/doc/SVM2CRM.Rnw
SVM2CRM/inst/doc/SVM2CRM.pdf
SVM2CRM/man
SVM2CRM/man/cisREfindbed.Rd
SVM2CRM/man/createBed.Rd
SVM2CRM/man/createSVMinput.Rd
SVM2CRM/man/featSelectionWithKmeans.Rd
SVM2CRM/man/findFeatureOverlap.Rd
SVM2CRM/man/frequencyHM.Rd
SVM2CRM/man/getSignal.Rd
SVM2CRM/man/performanceSVM.Rd
SVM2CRM/man/plotFscore.Rd
SVM2CRM/man/plotROC.Rd
SVM2CRM/man/predictionGW.Rd
SVM2CRM/man/smoothInputFS.Rd
SVM2CRM/man/tuningParametersCombROC.Rd
SVM2CRM/vignettes
SVM2CRM/vignettes/SVM2CRM.Rnw
SVM2CRM/vignettes/SVM2CRM.bib
SVM2CRM/vignettes/unsrturl.bst