Man pages for imbforge/encodeChIPqc
A set of useful ChIPseq QC metrics from the ENCODE project
| calculateBindingCharacteristics | Get binding characteristics |
| calculateIDR | Calculate irreproducibly discovery rate |
| callPeaks | Call peaks using SPP |
| encodeChIPqc-package | What the package does (short line) ~~ package title ~~ |
| frip | Fraction of reads in peaks |
| gAlignmentsToSppTags | Convert GAlignments object to SPP tags |
| getCrossConsistencyRatios | Get cross-consistency ratios |
| getSelfConsistencyRatios | Get self-consistency ratios |
| IPstrength | Plot IP strength |
| mser | Assess saturation properties |
| normalizeTagCount | Normalize tag counts |
| PBC | PCR bottleneck coefficient |
| pcaPlot | PCA plot of ChIP and input samples |
| phantomPeak | QC metrics RSC and NSC |
| plotIDR | plot irreproducible discovery rate |
| samplesHeatmap | Heatmap and cluster sample-sample distances |
| sppPeaksToGRanges | Convert output from SPP to GRanges object |
| tagCount | ChIP-seq binned tag counting tool |
| topHeatmap | Heatmap and cluster of top variant regions |
