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 |