Package: GeneBreak 1.37.0

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

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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'))

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

Datasets:

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

On BioConductor:GeneBreak-1.37.0(bioc 3.21)GeneBreak-1.36.0(bioc 3.20)

acgh copynumbervariation dnaseq genetics sequencing wholegenome visualization

4.60 score 2 stars 6 scripts 204 downloads 2 mentions 19 exports 52 dependencies

Last updated 2 months agofrom:3793a7cc39. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-win	NOTE	Nov 25 2024
R-4.5-linux	NOTE	Nov 25 2024
R-4.4-win	NOTE	Nov 25 2024
R-4.4-mac	NOTE	Nov 25 2024
R-4.3-win	NOTE	Nov 25 2024
R-4.3-mac	NOTE	Nov 25 2024

Exports:accessOptions addGeneAnnotation bpFilter bpGenes bpPlot bpStats breakpointData breakpointsPerGene callData featureChromosomes featureInfo featuresPerGene geneChromosomes geneInfo getBreakpoints namesFeatures recurrentGenes sampleNames segmentData

Dependencies:askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops CGHbase CGHcall codetools cpp11 crayon curl digest DNAcopy formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges globals httr impute IRanges jsonlite lambda.r limma listenv marray matrixStats mime openssl parallelly QDNAseq R.methodsS3 R.oo R.utils R6 Rhtslib Rsamtools S4Vectors snow snowfall statmod sys UCSC.utils XVector zlibbioc

GeneBreak

Rendered fromGeneBreak.Rnwusingutils::Sweaveon Nov 25 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Access Object Data. This method lists possible functions to access the data of the object.	accessOptions accessOptions,CopyNumberBreakPoints-method
addGeneAnnotation	addGeneAnnotation addGeneAnnotation,CopyNumberBreakPoints-method
bpFilter	bpFilter bpFilter,CopyNumberBreakPoints-method
bpGenes	bpGenes bpGenes,CopyNumberBreakPointGenes-method
bpPlot	bpPlot bpPlot,CopyNumberBreakPoints-method
bpStats	bpStats 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 chr18	copynumber.data.chr18
CGHcall Example copynumber data hg18 chr20	copynumber.data.chr20
CGHcall Example copynumber data hg18 chr21	copynumber.data.chr21
An S4 class to represent a CopyNumberBreakPointGenes object	CopyNumberBreakPointGenes CopyNumberBreakPointGenes-class
An S4 class to represent a CopyNumberBreakPoints object.	CopyNumberBreakPoints CopyNumberBreakPoints-class
Gene Annotation hg18	ens.gene.ann.hg18
Gene Annotation hg19	ens.gene.ann.hg19
Gene Annotation hg38	ens.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 data	GeneBreak-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
getBreakpoints	getBreakpoints
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