# GUIDE-seq and PEtag-seq analysis pipeline

## Documentation for package ‘GUIDEseq’ version 1.40.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

GUIDEseq-package | Analysis of GUIDE-seq
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
GUIDEseq | Analysis of GUIDE-seq
GUIDEseqAnalysis | Analysis pipeline for GUIDE-seq dataset
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
PEtagAnalysis | Analysis pipeline for PEtag-seq dataset
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