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| 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 |