BreakPoint              BreakPoint object
breakSeekr              Find breakpoints from deltaWs
breakpointR-package     Breakpoint detection in Strand-Seq data
breakpointr             Main function for the 'breakpointR' package
breakpointr2UCSC        Export UCSC browser formated files
collapseBins            Collapse consecutive bins with the same ID
                        value
confidenceInterval      Estimate confidence intervals for breakpoints
confidenceInterval.binomial
                        Estimate confidence intervals for breakpoints
createCompositeFile     Create composite Strand-seq file
deltaWCalculator        Calculate deltaWs
exportRegions           Function to print WC regions after breakpointR
                        analysis
genotyping              Set of functions to genotype regions in between
                        localized breakpoints
hotspotter              Find hotspots of genomic events
insertchr               Insert chromosome for in case it's missing
loadFromFiles           Load 'breakpointR' objects from file
plotBreakpoints         Plotting genome-wide ideograms 'breakpointR'
plotBreakpointsPerChr   Plotting chromosome specific ideograms
                        'breakpointR'
plotHeatmap             Genome wide heatmap of template inheritance
                        states
ranges2UCSC             Generates a bedfile from an input GRanges file
readBamFileAsGRanges    Import BAM file into GRanges
readConfig              Read BreakpointR configuration file
runBreakpointr          Find breakpoints in Strand-seq data
summarizeBreaks         Compile breakpoint summary table
synchronizeReadDir      Synchronize Strand-seq read directionality
transCoord              Transform genomic coordinates
writeConfig             Write BreakpointR configuration file
