Files in jianhong/ATACseqQC
ATAC-seq Quality Control
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/ATACseqQC.R
R/NFRscore.R
R/PTscore.R
R/TSSEscore.R
R/bamQC.R
R/distanceDyad.R
R/enrichedFragments.R
R/estimateLibComplexity.R
R/factorFootprints.R
R/footprintsScanner.R
R/fragSizeDist.R
R/peakDet.R
R/plotCorrelation.R
R/plotFootprints.R
R/pseudoPausingIndex.R
R/pwmscores.R
R/readBamFile.R
R/readsDupFreq.R
R/saturationPlot.R
R/shiftGAlignments.R
R/shiftGAlignmentsList.R
R/shiftReads.R
R/splitBam.R
R/splitGAlignmentsByCut.R
R/vPlot.R
R/writeListOfGAlignments.R
README.md
inst/CITATION
inst/extdata/GL1.bam
inst/extdata/GL1.bam.bai
inst/extdata/GL2.bam
inst/extdata/GL2.bam.bai
inst/extdata/GL3.bam
inst/extdata/GL3.bam.bai
inst/extdata/GL4.bam
inst/extdata/GL4.bam.bai
inst/extdata/IGVSnapshot.R
inst/extdata/jolma2013.motifs.bindingList.95.rds
inst/extdata/splited/NucleosomeFree.bam
inst/extdata/splited/NucleosomeFree.bam.bai
inst/extdata/splited/dinucleosome.bam
inst/extdata/splited/dinucleosome.bam.bai
inst/extdata/splited/mononucleosome.bam
inst/extdata/splited/mononucleosome.bam.bai
inst/extdata/splited/trinucleosome.bam
inst/extdata/splited/trinucleosome.bam.bai
man/ATACseqQC-package.Rd
man/DB.Rd
man/NFRscore.Rd
man/PTscore.Rd
man/TSSEscore.Rd
man/bamQC.Rd
man/distanceDyad.Rd
man/enrichedFragments.Rd
man/estimateLibComplexity.Rd
man/factorFootprints.Rd
man/footprintsScanner.Rd
man/fragSizeDist.Rd
man/peakdet.Rd
man/plotCorrelation.Rd
man/plotFootprints.Rd
man/pseudoPausingIndex.Rd
man/pwmscores.Rd
man/readBamFile.Rd
man/readsDupFreq.Rd
man/saturationPlot.Rd
man/shiftGAlignments.Rd
man/shiftGAlignmentsList.Rd
man/shiftReads.Rd
man/splitBam.Rd
man/splitGAlignmentsByCut.Rd
man/vPlot.Rd
man/writeListOfGAlignments.Rd
tests/.DS_Store
tests/runTests.R
tests/testthat/.DS_Store
tests/testthat/test_bamQC.R
tests/testthat/test_factorFootprints.R
tests/testthat/test_fragSizeDist.R
tests/testthat/test_shiftGAlignmentsList.R
tests/testthat/test_shiftReads.R
tests/testthat/test_splitGAlignmentsByCut.R
vignettes/ATACseqQC.Rmd
vignettes/CTCFfootprints.png
vignettes/CTCFvPlot.png
vignettes/bibliography.bib
vignettes/nature.csl
