API for imbforge/encodeChIPqc
A set of useful ChIPseq QC metrics from the ENCODE project
| Global functions | |
|---|---|
| .clusterApplyLB | Source code |
| IPstrength | Man page Source code |
| PBC | Man page Source code |
| calculateBindingCharacteristics | Man page Source code |
| calculateIDR | Man page Source code |
| callPeaks | Man page Source code |
| clayton.cop.den | Source code |
| clean.data | Source code |
| comp.ez.cutoff | Source code |
| comp.uri | Source code |
| comp.uri.ez | Source code |
| compute.pair.uri | Source code |
| concatenate.chr | Source code |
| d.binormal | Source code |
| deconcatenate.chr | Source code |
| e.step.2copula | Source code |
| e.step.2copula.value | Source code |
| e.step.2gaussian | Source code |
| e.step.2gaussian.value | Source code |
| e.step.2normal | Source code |
| em.2copula.quick | Source code |
| em.2gaussian.quick | Source code |
| em.transform | Source code |
| encodeChIPqc | Man page |
| encodeChIPqc-package | Man page |
| est.cdf.rank | Source code |
| est.mar.hist | Source code |
| fill.missing.peaks | Source code |
| find.mu.sigma | Source code |
| find.overlap | Source code |
| find.peaks | Source code |
| fit.1.component | Source code |
| fit.2copula.em | Source code |
| fit.clayton.1 | Source code |
| fit.em | Source code |
| fit.gaussian.1 | Source code |
| frip | Man page Source code |
| gAlignmentsToSppTags | Man page Source code |
| gaussian.cop.den | Source code |
| get.cdf | Source code |
| get.ez | Source code |
| get.ez.tt | Source code |
| get.ez.tt.all | Source code |
| get.hist.mean | Source code |
| get.hist.var | Source code |
| get.mar.mean | Source code |
| get.pdf | Source code |
| get.pdf.cdf | Source code |
| get.pseudo.mix | Source code |
| get.uri.2d | Source code |
| get.uri.matched | Source code |
| getCrossConsistencyRatios | Man page Source code |
| getSelfConsistencyRatios | Man page Source code |
| init | Source code |
| init.dist | Source code |
| loglik.2binormal | Source code |
| loglik.2copula | Source code |
| loglik.2copula.value | Source code |
| loglik.2gaussian.copula | Source code |
| loglik.2gaussian.copula.value | Source code |
| m.step.2copula | Source code |
| m.step.2copula.value | Source code |
| m.step.2gaussian | Source code |
| m.step.2gaussian.value | Source code |
| m.step.2gaussian.value2 | Source code |
| m.step.2normal | Source code |
| map.sig.value | Source code |
| merge.peaks | Source code |
| merge.peaks.best | Source code |
| mle.clayton.copula | Source code |
| mle.gaussian.copula | Source code |
| mser | Man page Source code |
| normalizeTagCount | Man page Source code |
| overlap.middle | Source code |
| pair.peaks | Source code |
| pair.peaks.filter | Source code |
| pcaPlot | Man page Source code |
| phantomPeak | Man page Source code |
| plot.ez.group | Source code |
| plot.uri.group | Source code |
| plotIDR | Man page Source code |
| process.narrowpeak | Source code |
| rm.unmatch | Source code |
| samplesHeatmap | Man page Source code |
| scale.t2n | Source code |
| sppPeaksToGRanges | Man page Source code |
| tagCount | Man page Source code |
| topHeatmap | Man page Source code |
