Package: GeneBreak 1.35.0

Evert van den Broek

GeneBreak: Gene Break Detection

Recurrent breakpoint gene detection on copy number aberration profiles.

Authors:Evert van den Broek, Stef van Lieshout

GeneBreak_1.35.0.tar.gz
GeneBreak_1.35.0.zip(r-4.5)GeneBreak_1.35.0.zip(r-4.4)GeneBreak_1.35.0.zip(r-4.3)
GeneBreak_1.35.0.tgz(r-4.4-any)GeneBreak_1.35.0.tgz(r-4.3-any)
GeneBreak_1.35.0.tar.gz(r-4.5-noble)GeneBreak_1.35.0.tar.gz(r-4.4-noble)
GeneBreak_1.35.0.tgz(r-4.4-emscripten)GeneBreak_1.35.0.tgz(r-4.3-emscripten)
GeneBreak.pdf |GeneBreak.html✨
GeneBreak/json (API)
NEWS

# Install 'GeneBreak' in R:
install.packages('GeneBreak', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/stefvanlieshout/genebreak/issues

Datasets:

On BioConductor:GeneBreak-1.35.0(bioc 3.20)GeneBreak-1.34.0(bioc 3.19)

bioconductor-package

19 exports 0.82 score 51 dependencies 2 mentions

Last updated 2 months agofrom:1b00bc94d6

Exports:accessOptionsaddGeneAnnotationbpFilterbpGenesbpPlotbpStatsbreakpointDatabreakpointsPerGenecallDatafeatureChromosomesfeatureInfofeaturesPerGenegeneChromosomesgeneInfogetBreakpointsnamesFeaturesrecurrentGenessampleNamessegmentData

Dependencies:askpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsCGHbaseCGHcallcodetoolscpp11crayoncurldigestDNAcopyformatRfutile.loggerfutile.optionsfuturefuture.applyGenomeInfoDbGenomeInfoDbDataGenomicRangesglobalshttrimputeIRangesjsonlitelambda.rlimmalistenvmarraymatrixStatsmimeopensslparallellyQDNAseqR.methodsS3R.ooR.utilsR6RhtslibRsamtoolsS4VectorssnowsnowfallstatmodsysUCSC.utilsXVectorzlibbioc

GeneBreak

Rendered fromGeneBreak.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2018-09-06
Started: 2015-10-07

Readme and manuals

Help Manual

Help pageTopics
Access Object Data. This method lists possible functions to access the data of the object.accessOptions accessOptions,CopyNumberBreakPoints-method
addGeneAnnotationaddGeneAnnotation addGeneAnnotation,CopyNumberBreakPoints-method
bpFilterbpFilter bpFilter,CopyNumberBreakPoints-method
bpGenesbpGenes bpGenes,CopyNumberBreakPointGenes-method
bpPlotbpPlot bpPlot,CopyNumberBreakPoints-method
bpStatsbpStats bpStats,CopyNumberBreakPoints-method
Access Object breakpointData. This method returns a dataframe with breakpoint values per feature.breakpointData breakpointData,CopyNumberBreakPoints-method
Access Object breakpointsPerGene. This method returns a dataframe with breakpoints per gene.breakpointsPerGene breakpointsPerGene,CopyNumberBreakPointGenes-method
Access Object callData. This method returns a dataframe with feature call values.callData callData,CopyNumberBreakPoints-method
CGHcall Example copynumber data hg18 chr18copynumber.data.chr18
CGHcall Example copynumber data hg18 chr20copynumber.data.chr20
CGHcall Example copynumber data hg18 chr21copynumber.data.chr21
An S4 class to represent a CopyNumberBreakPointGenes objectCopyNumberBreakPointGenes CopyNumberBreakPointGenes-class
An S4 class to represent a CopyNumberBreakPoints object.CopyNumberBreakPoints CopyNumberBreakPoints-class
Gene Annotation hg18ens.gene.ann.hg18
Gene Annotation hg19ens.gene.ann.hg19
Gene Annotation hg38ens.gene.ann.hg38
Access Object featureChromosomes. This method returns a vector with feature chromosomes.featureChromosomes featureChromosomes,CopyNumberBreakPoints-method
Access Options featureInfo. This method returns a dataframe with feature annotations.featureInfo featureInfo,CopyNumberBreakPoints-method
Access Object featuresPerGene. This method returns a vector with gene-related features for a particular gene.featuresPerGene featuresPerGene,CopyNumberBreakPointGenes-method
GeneBreak: A package for gene breakpoint detection on copy number abberation dataGeneBreak-package GeneBreak
Access Object geneChromosomes. This method returns a vector with gene chromosomes.geneChromosomes geneChromosomes,CopyNumberBreakPointGenes-method
Access Options geneInfo. This method returns a dataframe with gene annotations.geneInfo geneInfo,CopyNumberBreakPointGenes-method
getBreakpointsgetBreakpoints
Access Object namesFeatures. This method returns a vector with feature names.namesFeatures namesFeatures,CopyNumberBreakPoints-method
Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold.recurrentGenes recurrentGenes,CopyNumberBreakPointGenes-method
Access Object sampleNames. This method returns a vector with sample names.sampleNames sampleNames,CopyNumberBreakPoints-method
Access Object segmentData. This method returns a dataframe with segment values.segmentData segmentData,CopyNumberBreakPoints-method