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ATACseqQC-package
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ATAC-seq Quality Control |
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DB()
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helper function for differential binding |
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NFRscore()
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Nucleosome Free Regions (NFR) score |
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PTscore()
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Promoter/Transcript body (PT) score |
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TSSEscore()
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Transcription Start Site (TSS) Enrichment Score |
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bamQC()
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Mapping quality control |
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distanceDyad()
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Distance of potential nucleosome dyad |
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enrichedFragments()
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enrichment for nucleosome-free fragments and nucleosome signals |
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estimateLibComplexity()
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Library complexity estimation |
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factorFootprints()
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plot ATAC-seq footprints infer factor occupancy genome wide |
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footprintsScanner() prepareBindingSitesList()
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scan ATAC-seq footprints infer factor occupancy genome wide |
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fragSizeDist()
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fragment size distribution |
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peakdet()
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Detect peak positions |
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plotCorrelation()
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plot Correlations of multiple samples |
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plotFootprints()
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Plots a footprint estimated by Centipede |
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pwmscores()
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max PWM scores for sequences |
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readBamFile()
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read in bam files |
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readsDupFreq()
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Calculating duplication frequency |
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saturationPlot()
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Plotting Saturation curves |
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shiftGAlignments()
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shift 5' ends for single end reads |
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shiftGAlignmentsList()
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shift 5' ends |
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shiftReads()
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shift read for 5'end |
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splitBam()
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prepare bam files for downstream analysis |
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splitGAlignmentsByCut()
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split bams into nucleosome free, mononucleosome,
dinucleosome and trinucleosome |
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vPlot()
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V-plot |
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writeListOfGAlignments()
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export list of GAlignments into bam files |