Man pages for jianhong/ATACseqQC
ATAC-seq Quality Control
| ATACseqQC-package | 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... |
| 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 |
| 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... |
| TSSEscore | Transcription Start Site (TSS) Enrichment Score |
| vPlot | V-plot |
| writeListOfGAlignments | export list of GAlignments into bam files |
