# ATAC-seq Quality Control

## Documentation for package ‘ATACseqQC’ version 1.25.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ATACseqQC-package | ATAC-seq Quality Control
ATACseqQC | ATAC-seq Quality Control
bamQC | Mapping quality control
DB | helper function for differential binding
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
NFRscore | Nucleosome Free Regions (NFR) score
peakdet | Detect peak positions
plotCorrelation | plot Correlations of multiple samples
plotFootprints | Plots a footprint estimated by Centipede
prepareBindingSitesList | scan ATAC-seq footprints infer factor occupancy genome wide
pseudoPausingIndex | Simulation pausing index
PTscore | Promoter/Transcript body (PT) score
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
TSSEscore | Transcription Start Site (TSS) Enrichment Score
vPlot | V-plot
writeListOfGAlignments | export list of GAlignments into bam files