# ATAC-seq Quality Control

## Documentation for package ‘ATACseqQC’ version 1.2.0

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

## Help Pages

ATACseqQC-package | ATAC-seq Quality Control
ATACseqQC | ATAC-seq Quality Control
bamQC | Mapping quality control
enrichedFragments | enrichment for nucleosome-free fragments and nucleosome signals
factorFootprints | plot ATAC-seq footprints infer factor occupancy genome wide
fragSizeDist | fragment size distribution
plotFootprints | Plots a footprint estimated by Centipede
pwmscores | max PWM scores for sequences
readBamFile | read in bam files
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
writeListOfGAlignments | export list of GAlignments into bam files