GUIDE-seq and PEtag-seq analysis pipeline


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Documentation for package ‘GUIDEseq’ version 1.37.0

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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