GUIDEseq-package        Analysis of GUIDE-seq
GUIDEseqAnalysis        Analysis pipeline for GUIDE-seq dataset
PEtagAnalysis           Analysis pipeline for PEtag-seq dataset
annotateOffTargets      Annotate offtargets with gene name
buildFeatureVectorForScoringBulge
                        Build Feature Vector For Scoring Offtargets
                        with Bulge
combineOfftargets       Combine Offtargets
compareSamples          Compare Samples using Fisher's exact test
createBarcodeFasta      Create barcode as fasta file format for
                        building bowtie1 index
getBestAlnInfo          Parse pairwise alignment
getPeaks                Obtain peaks from GUIDE-seq
getUniqueCleavageEvents
                        Using UMI sequence to obtain the starting
                        sequence library
getUsedBarcodes         Create barcodes from the p5 and p7 index used
                        for each sequencing lane
mergePlusMinusPeaks     Merge peaks from plus strand and minus strand
offTargetAnalysisOfPeakRegions
                        Offtarget Analysis of GUIDE-seq peaks
offTargetAnalysisWithBulge
                        offTarget Analysis With Bulges Allowed Finding
                        offtargets around peaks from GUIDE-seq or
                        around any given genomic regions with bulges
                        allowed in gRNA or the DNA sequence of
                        offTargets when aligning gRNA and DNA
                        sequences.
peaks.gr                example cleavage sites
plotAlignedOfftargets   Plot offtargets aligned to the target sequence
plotHeatmapOfftargets   Plot offtargets from multiple samples as
                        heatmap
plotTracks              Plot offtargets as manhantann plots or along
                        all chromosomes with one track per chromosome,
                        or scatter plot for two selected measurements
uniqueCleavageEvents    example unique cleavage sites
