|ATACseqQC-package||ATAC-seq Quality Control|
|enrichedFragments||enrichment for nucleosome-free fragments and nucleosome...|
|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...|
|writeListOfGAlignments||export list of GAlignments into bam files|
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