GeneBreak: Gene Break Detection

Recurrent breakpoint gene detection on copy number aberration profiles.

AuthorEvert van den Broek, Stef van Lieshout
Date of publicationNone
MaintainerEvert van den Broek <vandenbroek.evert@gmail.com>
LicenseGPL-2
Version1.4.0
https://github.com/stefvanlieshout/GeneBreak

View on Bioconductor

Man pages

accessOptions-CopyNumberBreakPoints-method: Access Object Data. This method lists possible functions to...

addGeneAnnotation-CopyNumberBreakPoints-method: addGeneAnnotation

bpFilter-CopyNumberBreakPoints-method: bpFilter

bpGenes-CopyNumberBreakPointGenes-method: bpGenes

bpPlot-CopyNumberBreakPoints-method: bpPlot

bpStats-CopyNumberBreakPoints-method: bpStats

breakpointData-CopyNumberBreakPoints-method: Access Object breakpointData. This method returns a dataframe...

breakpointsPerGene-CopyNumberBreakPointGenes-method: Access Object breakpointsPerGene. This method returns a...

callData-CopyNumberBreakPoints-method: Access Object callData. This method returns a dataframe with...

CopyNumberBreakPointGenes-class: An S4 class to represent a CopyNumberBreakPointGenes object

CopyNumberBreakPoints-class: An S4 class to represent a CopyNumberBreakPoints object.

copynumber.data.chr18: CGHcall Example copynumber data hg18 chr18

copynumber.data.chr20: CGHcall Example copynumber data hg18 chr20

copynumber.data.chr21: CGHcall Example copynumber data hg18 chr21

ens.gene.ann.hg18: Gene Annotation hg18

ens.gene.ann.hg19: Gene Annotation hg19

ens.gene.ann.hg38: Gene Annotation hg38

featureChromosomes-CopyNumberBreakPoints-method: Access Object featureChromosomes. This method returns a...

featureInfo-CopyNumberBreakPoints-method: Access Options featureInfo. This method returns a dataframe...

featuresPerGene-CopyNumberBreakPointGenes-method: Access Object featuresPerGene. This method returns a vector...

GeneBreak: GeneBreak: A package for gene breakpoint detection on copy...

geneChromosomes-CopyNumberBreakPointGenes-method: Access Object geneChromosomes. This method returns a vector...

geneInfo-CopyNumberBreakPointGenes-method: Access Options geneInfo. This method returns a dataframe with...

getBreakpoints: getBreakpoints

namesFeatures-CopyNumberBreakPoints-method: Access Object namesFeatures. This method returns a vector...

recurrentGenes-CopyNumberBreakPointGenes-method: Access Options recurrentGenes. This method returns a...

sampleNames-CopyNumberBreakPoints-method: Access Object sampleNames. This method returns a vector with...

segmentData-CopyNumberBreakPoints-method: Access Object segmentData. This method returns a dataframe...

Functions

accessOptions Man page
accessOptions,CopyNumberBreakPoints-method Man page
addGeneAnnotation Man page
addGeneAnnotation,CopyNumberBreakPoints-method Man page
bpFilter Man page
bpFilter,CopyNumberBreakPoints-method Man page
bpGenes Man page
bpGenes,CopyNumberBreakPointGenes-method Man page
bpPlot Man page
bpPlot,CopyNumberBreakPoints-method Man page
bpStats Man page
bpStats,CopyNumberBreakPoints-method Man page
breakpointData Man page
breakpointData,CopyNumberBreakPoints-method Man page
breakpointsPerGene Man page
breakpointsPerGene,CopyNumberBreakPointGenes-method Man page
callData Man page
callData,CopyNumberBreakPoints-method Man page
CopyNumberBreakPointGenes Man page
CopyNumberBreakPointGenes-class Man page
CopyNumberBreakPoints Man page
CopyNumberBreakPoints-class Man page
copynumber.data.chr18 Man page
copynumber.data.chr20 Man page
copynumber.data.chr21 Man page
ens.gene.ann.hg18 Man page
ens.gene.ann.hg19 Man page
ens.gene.ann.hg38 Man page
featureChromosomes Man page
featureChromosomes,CopyNumberBreakPoints-method Man page
featureInfo Man page
featureInfo,CopyNumberBreakPoints-method Man page
featuresPerGene Man page
featuresPerGene,CopyNumberBreakPointGenes-method Man page
GeneBreak Man page
GeneBreak-package Man page
geneChromosomes Man page
geneChromosomes,CopyNumberBreakPointGenes-method Man page
geneInfo Man page
geneInfo,CopyNumberBreakPointGenes-method Man page
getBreakpoints Man page
namesFeatures Man page
namesFeatures,CopyNumberBreakPoints-method Man page
recurrentGenes Man page
recurrentGenes,CopyNumberBreakPointGenes-method Man page
sampleNames Man page
sampleNames,CopyNumberBreakPoints-method Man page
segmentData Man page
segmentData,CopyNumberBreakPoints-method Man page

Files

GeneBreak/DESCRIPTION
GeneBreak/NAMESPACE
GeneBreak/NEWS
GeneBreak/R
GeneBreak/R/AllClasses.R GeneBreak/R/AllGenerics.R GeneBreak/R/GeneBreakAccessors.R GeneBreak/R/GeneBreakMethods.R GeneBreak/R/dataDocumentation.R GeneBreak/R/pkgname.R GeneBreak/R/private.R
GeneBreak/README.md
GeneBreak/build
GeneBreak/build/vignette.rds
GeneBreak/data
GeneBreak/data/copynumber.data.chr18.rda
GeneBreak/data/copynumber.data.chr20.rda
GeneBreak/data/copynumber.data.chr21.rda
GeneBreak/data/datalist
GeneBreak/data/ens.gene.ann.hg18.rda
GeneBreak/data/ens.gene.ann.hg19.rda
GeneBreak/data/ens.gene.ann.hg38.rda
GeneBreak/inst
GeneBreak/inst/doc
GeneBreak/inst/doc/GeneBreak.R
GeneBreak/inst/doc/GeneBreak.Rnw
GeneBreak/inst/doc/GeneBreak.pdf
GeneBreak/man
GeneBreak/man/CopyNumberBreakPointGenes-class.Rd GeneBreak/man/CopyNumberBreakPoints-class.Rd GeneBreak/man/GeneBreak.Rd GeneBreak/man/accessOptions-CopyNumberBreakPoints-method.Rd GeneBreak/man/addGeneAnnotation-CopyNumberBreakPoints-method.Rd GeneBreak/man/bpFilter-CopyNumberBreakPoints-method.Rd GeneBreak/man/bpGenes-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/bpPlot-CopyNumberBreakPoints-method.Rd GeneBreak/man/bpStats-CopyNumberBreakPoints-method.Rd GeneBreak/man/breakpointData-CopyNumberBreakPoints-method.Rd GeneBreak/man/breakpointsPerGene-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/callData-CopyNumberBreakPoints-method.Rd GeneBreak/man/copynumber.data.chr18.Rd GeneBreak/man/copynumber.data.chr20.Rd GeneBreak/man/copynumber.data.chr21.Rd GeneBreak/man/ens.gene.ann.hg18.Rd GeneBreak/man/ens.gene.ann.hg19.Rd GeneBreak/man/ens.gene.ann.hg38.Rd GeneBreak/man/featureChromosomes-CopyNumberBreakPoints-method.Rd GeneBreak/man/featureInfo-CopyNumberBreakPoints-method.Rd GeneBreak/man/featuresPerGene-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/geneChromosomes-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/geneInfo-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/getBreakpoints.Rd GeneBreak/man/namesFeatures-CopyNumberBreakPoints-method.Rd GeneBreak/man/recurrentGenes-CopyNumberBreakPointGenes-method.Rd GeneBreak/man/sampleNames-CopyNumberBreakPoints-method.Rd GeneBreak/man/segmentData-CopyNumberBreakPoints-method.Rd
GeneBreak/vignettes
GeneBreak/vignettes/GeneBreak.Rnw

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