Package: breakpointR 1.25.0

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_1.25.0.tar.gz
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breakpointR.pdf |breakpointR.html✨
breakpointR/json (API)
NEWS

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

Peer review:

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

On BioConductor:breakpointR-1.23.0(bioc 3.20)breakpointR-1.22.0(bioc 3.19)

softwaresequencingdnaseqsinglecellcoverage

5.60 score 8 stars 10 scripts 301 downloads 19 exports 73 dependencies

Last updated 23 days agofrom:da582c9ce8. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:breakpointrbreakpointr2UCSCbreakSeekrdeltaWCalculatorexportRegionsgenotype.binomgenotype.fisherGenotypeBreakshotspotterloadFromFilesplotBreakpointsplotBreakpointsPerChrplotHeatmapranges2UCSCreadBamFileAsGRangesremoveReadPileupSpikesrunBreakpointrsummarizeBreakssynchronizeReadDir

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbreakpointRdataclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArraydoParallelfansifarverforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

How to use breakpointR

Rendered frombreakpointR.Rnwusingknitr::knitron Oct 30 2024.

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