Man pages for daewoooo/breakpointR
Find breakpoints in Strand-seq data

BreakPointBreakPoint object
breakpointrMain function for the 'breakpointR' package
breakpointr2UCSCExport UCSC browser formated files
breakpointR-packageBreakpoint detection in Strand-Seq data
breakSeekrFind breakpoints from deltaWs
collapseBinsCollapse consecutive bins with the same ID value
confidenceIntervalEstimate confidence intervals for breakpoints
confidenceInterval.binomialEstimate confidence intervals for breakpoints
createCompositeFileCreate composite Strand-seq file
deltaWCalculatorCalculate deltaWs
deltaWCalculatorVariousWindowsCalculate deltaWs using various window sizes
exportRegionsFunction to print WC regions after breakpointR analysis
genotype.binomAssign states to any given region using binomial test.
genotype.fisherAssign states to any given region using Fisher Exact Test.
genotypingSet of functions to genotype regions in between localized...
hotspotterFind hotspots of genomic events
insertchrInsert chromosome for in case it's missing
loadFromFilesLoad 'breakpointR' objects from file
plotBreakpointsPlotting genome-wide ideograms 'breakpointR'
plotBreakpointsPerChrPlotting chromosome specific ideograms 'breakpointR'
plotHeatmapGenome wide heatmap of template inheritance states
ranges2UCSCGenerates a bedfile from an input GRanges file
readBamFileAsGRangesImport BAM file into GRanges
readConfigRead breakpointR configuration file
removeDoubleSCEsProcess double SCE chromosomes: with internal WC region.
removeReadPileupSpikesRemove large spikes in short reads coverage
runBreakpointrFind breakpoints in Strand-seq data
summarizeBreaksCompile breakpoint summary table
synchronizeReadDirSynchronize Strand-seq read directionality
transCoordTransform genomic coordinates
writeConfigWrite breakpointR configuration file
daewoooo/breakpointR documentation built on April 20, 2023, 4:13 p.m.