ATACseqQC-package       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
