GUIDE-seq and PEtag-seq analysis pipeline

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Documentation for package ‘GUIDEseq’ version 1.39.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• 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