Package: breakpointR 1.30.0

David Porubsky

breakpointR: Find breakpoints in Strand-seq data

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

Authors:David Porubsky, Ashley Sanders, Aaron Taudt

breakpointR_1.30.0.tar.gz
breakpointR_1.30.0.zip(r-4.7)breakpointR_1.30.0.zip(r-4.6)breakpointR_1.30.0.zip(r-4.5)
breakpointR_1.30.0.tgz(r-4.6-any)breakpointR_1.30.0.tgz(r-4.5-any)
breakpointR_1.30.0.tar.gz(r-4.7-any)breakpointR_1.30.0.tar.gz(r-4.6-any)
breakpointR_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
breakpointR/json (API)
NEWS

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

Bug tracker:https://github.com/daewoooo/breakpointr/issues

On BioConductor:breakpointR-1.31.0(bioc 3.24)breakpointR-1.30.0(bioc 3.23)

softwaresequencingdnaseqsinglecellcoverage

5.93 score 9 stars 19 scripts 446 downloads 19 exports 64 dependencies

Last updated from:c6194609a7 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR161
linux-devel-x86_64NOTE356
source / vignettesOK320
linux-release-x86_64NOTE384
macos-release-arm64NOTE260
macos-oldrel-arm64NOTE257
windows-develNOTE306
windows-releaseNOTE288
windows-oldrelNOTE293
wasm-releaseOK145

Exports:breakpointrbreakpointr2UCSCbreakSeekrdeltaWCalculatorexportRegionsgenotype.binomgenotype.fisherGenotypeBreakshotspotterloadFromFilesplotBreakpointsplotBreakpointsPerChrplotHeatmapranges2UCSCreadBamFileAsGRangesremoveReadPileupSpikesrunBreakpointrsummarizeBreakssynchronizeReadDir

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbreakpointRdatacigarilloclicodetoolscowplotcpp11crayoncurlDelayedArraydoParallelfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRhtslibrlangRsamtoolsS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsviridisLitewithrXVector

How to use breakpointR

Rendered frombreakpointR.Rnwusingknitr::knitron May 31 2026.

Last update: 2019-08-04
Started: 2017-03-31

Readme and manuals

Help Manual

Help pageTopics
Breakpoint detection in Strand-Seq databreakpointR-package breakpointR
BreakPoint objectBreakPoint
Main function for the 'breakpointR' packagebreakpointr
Export UCSC browser formated filesbreakpointr2UCSC
Find breakpoints from deltaWsbreakSeekr
Collapse consecutive bins with the same ID valuecollapseBins
Estimate confidence intervals for breakpointsconfidenceInterval
Estimate confidence intervals for breakpointsconfidenceInterval.binomial
Create composite Strand-seq filecreateCompositeFile
Calculate deltaWsdeltaWCalculator
Calculate deltaWs using various window sizesdeltaWCalculatorVariousWindows
Function to print WC regions after breakpointR analysisexportRegions
Assign states to any given region using binomial test.genotype.binom
Assign states to any given region using Fisher Exact Test.genotype.fisher
Set of functions to genotype regions in between localized breakpointsGenotypeBreaks genotyping
Find hotspots of genomic eventshotspotter
Insert chromosome for in case it's missinginsertchr
Load 'breakpointR' objects from fileloadFromFiles
Plotting genome-wide ideograms 'breakpointR'plotBreakpoints
Plotting chromosome specific ideograms 'breakpointR'plotBreakpointsPerChr
Genome wide heatmap of template inheritance statesplotHeatmap
Generates a bedfile from an input GRanges fileranges2UCSC
Import BAM file into GRangesreadBamFileAsGRanges
Read breakpointR configuration filereadConfig
Process double SCE chromosomes: with internal WC region.removeDoubleSCEs
Remove large spikes in short reads coverageremoveReadPileupSpikes
Find breakpoints in Strand-seq datarunBreakpointr
Compile breakpoint summary tablesummarizeBreaks
Synchronize Strand-seq read directionalitysynchronizeReadDir
Transform genomic coordinatestransCoord
Write breakpointR configuration filewriteConfig