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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GUIDEseq")
AuthorLihua Julie Zhu, Michael Lawrence, Ankit Gupta, Alper Kucukural, Manuel Garber, Scot A. Wolfe
Bioconductor views CRISPR GeneRegulation Sequencing WorkflowStep
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>
LicenseGPL (>= 2)
Version1.6.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/GUIDEseq-internal.R R/GUIDEseqAnalysis.R R/annotateOfftargets.R R/combineOfftargets.R R/createBarcodeFasta.R R/getPeaks.R R/getUniqueCleavageEvents.R R/getUsedBarcodes.R R/mergePlusMinusPeaks.R R/offTargetAnalysisOfPeakRegions.R
build
build/vignette.rds
data
data/peaks.gr.rda
data/uniqueCleavageEvents.rda
inst
inst/NEWS
inst/doc
inst/doc/GUIDEseq.R
inst/doc/GUIDEseq.Rnw
inst/doc/GUIDEseq.pdf
inst/extdata
inst/extdata/T2.fa
inst/extdata/T2plus100OffTargets.bed
inst/extdata/UMI-HEK293_site4_R1.txt
inst/extdata/UMI-HEK293_site4_chr13.txt
inst/extdata/bowtie2.HEK293_site4.sort.bed
inst/extdata/bowtie2.HEK293_site4_chr13.sort.bam
inst/extdata/bowtie2.HEK293_site4_chr13.sort.bed
inst/extdata/gRNA.fa
inst/extdata/p5.index
inst/extdata/p7.index
inst/extdata/sample1-17
inst/extdata/sample1-17/offTargetsInPeakRegions.xls
inst/extdata/sample2-18
inst/extdata/sample2-18/offTargetsInPeakRegions.xls
inst/extdata/sample3-19
inst/extdata/sample3-19/offTargetsInPeakRegions.xls
inst/extdata/sample4-20
inst/extdata/sample4-20/offTargetsInPeakRegions.xls
inst/extdata/sample5-21
inst/extdata/sample5-21/offTargetsInPeakRegions.xls
inst/extdata/sample6-22
inst/extdata/sample6-22/offTargetsInPeakRegions.xls
inst/extdata/sample7-23
inst/extdata/sample7-23/offTargetsInPeakRegions.xls
inst/extdata/testPeaks.rda
inst/extdata/testbothRunSum.rda
man
man/GUIDEseq-package.Rd man/GUIDEseqAnalysis.Rd man/annotateOffTargets.Rd man/combineOfftargets.Rd man/createBarcodeFasta.Rd man/getPeaks.Rd man/getUniqueCleavageEvents.Rd man/getUsedBarcodes.Rd man/mergePlusMinusPeaks.Rd man/offTargetAnalysisOfPeakRegions.Rd man/peaks.gr.Rd man/uniqueCleavageEvents.Rd
vignettes
vignettes/GUIDEseq.Rnw
Spark Online Training by Edureka

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

Please suggest features or report bugs with the GitHub issue tracker.

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