Files in LihuaJulieZhu/GUIDEseq
GUIDE-seq and PEtag-seq analysis pipeline
DESCRIPTION
NAMESPACE
R/GUIDEseq-internal.R
R/GUIDEseq-package.R
R/GUIDEseqAnalysis.R
R/PEtagAnalysis.R
R/annotateOfftargets.R
R/buildFeatureVectorForScoringBulge.R
R/bulge-internal.R
R/combineOfftargets.R
R/compareSamples.R
R/createBarcodeFasta.R
R/getAlnWithBulge.R
R/getBestAlnInfo.R
R/getPeaks.R
R/getUniqueCleavageEvents.R
R/getUsedBarcodes.R
R/mergePlusMinusPeaks.R
R/offTargetAnalysisOfPeakRegions.R
R/offTargetAnalysisWithBulge.R
R/plotAlignedOfftargets.R
R/plotHeatmapOfftargets.R
R/plotTracks.R
data/peaks.gr.rda
data/uniqueCleavageEvents.rda
inst/CITATION
inst/NEWS
inst/extdata/1450-PlusMinusPeaksMerged.bed
inst/extdata/1450-chr14-chr2-bulge-test.bed
inst/extdata/1450.fa
inst/extdata/1450peakSeq.RDS
inst/extdata/InsertionInOfftarget.RDS
inst/extdata/NatureBiot2016SuppTable19DoenchRoot.xlsx
inst/extdata/OT71_Bulge_example.xlsx
inst/extdata/PEtagAnalysis_testthat.RDS
inst/extdata/T2.fa
inst/extdata/T2plus100OffTargets.bed
inst/extdata/UMI-HEK293_site4_R1.txt
inst/extdata/UMI-HEK293_site4_chr13.txt
inst/extdata/UMI-testGetUmi.fastq
inst/extdata/alns.RDS
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/cleavages_testthat.RDS
inst/extdata/consecutiveDNABulge.RDS
inst/extdata/consecutiveDNABulge.bed
inst/extdata/consecutiveDNABulge2.RDS
inst/extdata/forVisualization/mergedOffTargets.txt
inst/extdata/forVisualization/offTargetsInPeakRegions.xls
inst/extdata/gRNA-PlusMinusPeaksMerged.bed
inst/extdata/gRNA.fa
inst/extdata/getUmi.pl
inst/extdata/p5.index
inst/extdata/p7.index
inst/extdata/pa.f.RDS
inst/extdata/pa.r.RDS
inst/extdata/sample1-17/offTargetsInPeakRegions.xls
inst/extdata/sample2-18/offTargetsInPeakRegions.xls
inst/extdata/sample3-19/offTargetsInPeakRegions.xls
inst/extdata/sample4-20/offTargetsInPeakRegions.xls
inst/extdata/sample5-21/offTargetsInPeakRegions.xls
inst/extdata/sample6-22/offTargetsInPeakRegions.xls
inst/extdata/sample7-23/offTargetsInPeakRegions.xls
inst/extdata/subjects2.RDS
inst/extdata/testCFDscoringWithBulge.RDS
inst/extdata/testGetUmi/testGetUmi.fastq
inst/extdata/testPeaks.rda
inst/extdata/testbothRunSum.rda
man/GUIDEseq-package.Rd
man/GUIDEseqAnalysis.Rd
man/PEtagAnalysis.Rd
man/annotateOffTargets.Rd
man/buildFeatureVectorForScoringBulge.Rd
man/combineOfftargets.Rd
man/compareSamples.Rd
man/createBarcodeFasta.Rd
man/getBestAlnInfo.Rd
man/getPeaks.Rd
man/getUniqueCleavageEvents.Rd
man/getUsedBarcodes.Rd
man/mergePlusMinusPeaks.Rd
man/offTargetAnalysisOfPeakRegions.Rd
man/offTargetAnalysisWithBulge.Rd
man/peaks.gr.Rd
man/plotAlignedOfftargets.Rd
man/plotHeatmapOfftargets.Rd
man/plotTracks.Rd
man/uniqueCleavageEvents.Rd
tests/testthat.R
tests/testthat/test-GUIDEseqAnalysis.R
tests/testthat/test-PEtagAnalysis.R
tests/testthat/test-buildFeatureVectorForScoringBulge.R
tests/testthat/test-getAlnWithBulge.R
tests/testthat/test-getBestAlnInfo.R
tests/testthat/test-getUniqueCleavageEvents.R
tests/testthat/test-internal_bulge.R
tests/testthat/test-offTargetAnalysisWithBulge.R
vignettes/GUIDEseq.Rnw
