Man pages for jianhong/ATACseqQC
ATAC-seq Quality Control

ATACseqQC-packageATAC-seq Quality Control
bamQCMapping quality control
distanceDyadDistance of potential nucleosome dyad
enrichedFragmentsenrichment for nucleosome-free fragments and nucleosome...
estimateLibComplexityLibrary complexity estimation
factorFootprintsplot ATAC-seq footprints infer factor occupancy genome wide
footprintsScannerscan ATAC-seq footprints infer factor occupancy genome wide
fragSizeDistfragment size distribution
IGVSnapshotTake IGV snapshots
NFRscoreNucleosome Free Regions (NFR) score
peakdetDetect peak positions
plotCorrelationplot Correlations of multiple samples
plotFootprintsPlots a footprint estimated by Centipede
prepareBindingSitesListhelper function for preparing the binding list
PTscorePromoter/Transcript body (PT) score
pwmscoresmax PWM scores for sequences
readBamFileread in bam files
readsDupFreqCalculating duplication frequency
saturationPlotPlotting Saturation curves
shiftGAlignmentsListshift 5' ends
shiftReadsshift read for 5'end
splitBamprepare bam files for downstream analysis
splitGAlignmentsByCutsplit bams into nucleosome free, mononucleosome, dinucleosome...
writeListOfGAlignmentsexport list of GAlignments into bam files
jianhong/ATACseqQC documentation built on Jan. 20, 2018, 11:46 p.m.