SVM2CRM: SVM2CRM: support vector machine for cis-regulatory elements detections
Version 1.8.0

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

AuthorGuidantonio Malagoli Tagliazucchi <malagoli@ingm.org>
Bioconductor views ChIPSeq ChipOnChip Preprocessing Software SupportVectorMachine
Date of publicationNone
MaintainerGuidantonio Malagoli Tagliazucchi <guidantonio.malagolitagliazucchi@unimore.it>
LicenseGPL-3
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SVM2CRM")

Popular man pages

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
plotFscore: Plot the F-score in relation with the sensitivity and...
smoothInputFS: Smooth the signals of the histone marks to prepare the input...
tuningParametersCombROC: Test different models using different kernel of SVM, values...
See all...

All man pages Function index File listing

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...

Functions

cisREfindbed Man page Man page Source code
createBed Man page Man page Source code
createSVMinput Man page Man page Source code
featSelectionWithKmeans Man page Man page Source code
findFeatureOverlap Man page Man page Source code
frequencyHM Man page Man page Source code
getSignal Man page Man page Source code
performanceSVM Man page Man page Source code
plotFscore Man page Man page Source code
plotROC Man page Man page Source code
predictionGW Man page Man page Source code
smoothInputFS Man page Man page Source code
tuningParametersCombROC Man page Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/cisREfindbed.R
R/createBed.R
R/createSVMinput.R
R/featSelectionWithKmeans.R
R/findFeatureOverlap.R
R/frequencyHM.R
R/getSignal.R
R/performanceSVM.R
R/plotFscore.R
R/plotROC.R
R/predictionGW.R
R/smoothInputFS.R
R/tuningParametersCombROC.R
README
build
build/vignette.rds
inst
inst/doc
inst/doc/SVM2CRM.R
inst/doc/SVM2CRM.Rnw
inst/doc/SVM2CRM.pdf
man
man/cisREfindbed.Rd
man/createBed.Rd
man/createSVMinput.Rd
man/featSelectionWithKmeans.Rd
man/findFeatureOverlap.Rd
man/frequencyHM.Rd
man/getSignal.Rd
man/performanceSVM.Rd
man/plotFscore.Rd
man/plotROC.Rd
man/predictionGW.Rd
man/smoothInputFS.Rd
man/tuningParametersCombROC.Rd
vignettes
vignettes/SVM2CRM.Rnw
vignettes/SVM2CRM.bib
vignettes/unsrturl.bst
SVM2CRM documentation built on May 20, 2017, 10:56 p.m.

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