ATACseqQC-package       ATAC-seq Quality Control
DB                      helper function for differential binding
NFRscore                Nucleosome Free Regions (NFR) score
PTscore                 Promoter/Transcript body (PT) score
TSSEscore               Transcription Start Site (TSS) Enrichment Score
bamQC                   Mapping quality control
distanceDyad            Distance of potential nucleosome dyad
enrichedFragments       enrichment for nucleosome-free fragments and
                        nucleosome signals
estimateLibComplexity   Library complexity estimation
factorFootprints        plot ATAC-seq footprints infer factor occupancy
                        genome wide
footprintsScanner       scan ATAC-seq footprints infer factor occupancy
                        genome wide
fragSizeDist            fragment size distribution
peakdet                 Detect peak positions
plotCorrelation         plot Correlations of multiple samples
plotFootprints          Plots a footprint estimated by Centipede
pseudoPausingIndex      Simulation pausing index
pwmscores               max PWM scores for sequences
readBamFile             read in bam files
readsDupFreq            Calculating duplication frequency
saturationPlot          Plotting Saturation curves
shiftGAlignments        shift 5' ends for single end reads
shiftGAlignmentsList    shift 5' ends
shiftReads              shift read for 5'end
splitBam                prepare bam files for downstream analysis
splitGAlignmentsByCut   split bams into nucleosome free,
                        mononucleosome, dinucleosome and trinucleosome
vPlot                   V-plot
writeListOfGAlignments
                        export list of GAlignments into bam files
