GeneBreak: Gene Break Detection

Share:

Recurrent breakpoint gene detection on copy number aberration profiles.

Author
Evert van den Broek, Stef van Lieshout
Date of publication
None
Maintainer
Evert van den Broek <vandenbroek.evert@gmail.com>
License
GPL-2
Version
1.4.0
URLs

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...

Files in this package

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