GUIDEseq: GUIDE-seq analysis pipeline

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.

AuthorLihua Julie Zhu, Michael Lawrence, Ankit Gupta, Alper Kucukural, Manuel Garber, Scot A. Wolfe
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>
LicenseGPL (>= 2)
Version1.4.1

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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