ATAC-seq Quality Control


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Documentation for package ‘ATACseqQC’ version 1.32.0

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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