GUIDEseq: GUIDE-seq analysis pipeline

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The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.

Author
Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Alper Kucukural, Manuel Garber, Scot A. Wolfe
Date of publication
None
Maintainer
Lihua Julie Zhu <julie.zhu@umassmed.edu>
License
GPL (>= 2)
Version
1.4.0

View on Bioconductor

Man pages

annotateOffTargets
Annotate offtargets with gene name
combineOfftargets
Combine Offtargets
getPeaks
Obtain peaks from GUIDE-seq
getUniqueCleavageEvents
Using UMI sequence to obtain the starting sequence library
GUIDEseqAnalysis
Analysis pipeline for GUIDE-seq dataset
GUIDEseq-package
Analysis of GUIDE-seq
mergePlusMinusPeaks
Merge peaks from plus strand and minus strand
offTargetAnalysisOfPeakRegions
Offtarget Analysis of GUIDE-seq peaks
peaks.gr
example cleavage sites
uniqueCleavageEvents
example unique cleavage sites

Files in this package

GUIDEseq/DESCRIPTION
GUIDEseq/NAMESPACE
GUIDEseq/R
GUIDEseq/R/GUIDEseq-internal.R
GUIDEseq/R/GUIDEseqAnalysis.R
GUIDEseq/R/annotateOfftargets.R
GUIDEseq/R/combineOfftargets.R
GUIDEseq/R/getPeaks.R
GUIDEseq/R/getUniqueCleavageEvents.R
GUIDEseq/R/mergePlusMinusPeaks.R
GUIDEseq/R/offTargetAnalysisOfPeakRegions.R
GUIDEseq/build
GUIDEseq/build/vignette.rds
GUIDEseq/data
GUIDEseq/data/peaks.gr.rda
GUIDEseq/data/uniqueCleavageEvents.rda
GUIDEseq/inst
GUIDEseq/inst/NEWS
GUIDEseq/inst/doc
GUIDEseq/inst/doc/GUIDEseq.R
GUIDEseq/inst/doc/GUIDEseq.Rnw
GUIDEseq/inst/doc/GUIDEseq.pdf
GUIDEseq/inst/extdata
GUIDEseq/inst/extdata/T2.fa
GUIDEseq/inst/extdata/T2plus100OffTargets.bed
GUIDEseq/inst/extdata/UMI-HEK293_site4_R1.txt
GUIDEseq/inst/extdata/UMI-HEK293_site4_chr13.txt
GUIDEseq/inst/extdata/bowtie2.HEK293_site4.sort.bed
GUIDEseq/inst/extdata/bowtie2.HEK293_site4_chr13.sort.bam
GUIDEseq/inst/extdata/bowtie2.HEK293_site4_chr13.sort.bed
GUIDEseq/inst/extdata/gRNA.fa
GUIDEseq/inst/extdata/sample1-17
GUIDEseq/inst/extdata/sample1-17/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample2-18
GUIDEseq/inst/extdata/sample2-18/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample3-19
GUIDEseq/inst/extdata/sample3-19/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample4-20
GUIDEseq/inst/extdata/sample4-20/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample5-21
GUIDEseq/inst/extdata/sample5-21/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample6-22
GUIDEseq/inst/extdata/sample6-22/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/sample7-23
GUIDEseq/inst/extdata/sample7-23/offTargetsInPeakRegions.xls
GUIDEseq/inst/extdata/testPeaks.rda
GUIDEseq/inst/extdata/testbothRunSum.rda
GUIDEseq/man
GUIDEseq/man/GUIDEseq-package.Rd
GUIDEseq/man/GUIDEseqAnalysis.Rd
GUIDEseq/man/annotateOffTargets.Rd
GUIDEseq/man/combineOfftargets.Rd
GUIDEseq/man/getPeaks.Rd
GUIDEseq/man/getUniqueCleavageEvents.Rd
GUIDEseq/man/mergePlusMinusPeaks.Rd
GUIDEseq/man/offTargetAnalysisOfPeakRegions.Rd
GUIDEseq/man/peaks.gr.Rd
GUIDEseq/man/uniqueCleavageEvents.Rd
GUIDEseq/vignettes
GUIDEseq/vignettes/GUIDEseq.Rnw