breakpointR-package | Breakpoint detection in Strand-Seq data |
BreakPoint | BreakPoint object |
breakpointR | Breakpoint detection in Strand-Seq data |
breakpointr | Main function for the 'breakpointR' package |
breakpointr2UCSC | Export UCSC browser formated files |
breakSeekr | Find breakpoints from deltaWs |
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 |
genotype.fisher | Set of functions to genotype regions in between localized breakpoints |
GenotypeBreaks | Set of functions to genotype regions in between localized breakpoints |
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 |