| basesCovered | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| chipseqFilter | Filtering ChIP-seq reads |
| coverageplot | Plot coverage on a small interval. |
| cstest | A test ChIP-Seq dataset |
| densityCorr | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| densityCorr,GenomicRanges | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| densityCorr,list | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| diffPeakSummary | A function to identify and produce summary statistics for differentially expressed peaks. |
| diffPeakSummary-method | A function to identify and produce summary statistics for differentially expressed peaks. |
| estimate.mean.fraglen | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| islandDepthPlot | Plot island depth distribution |
| laneSubsample | Subsample short read alignment locations |
| peakCutoff | Calculate a peak cutoff |
| peakSummary | Summarizing peak sets |
| peakSummary-method | Summarizing peak sets |
| peakSummary-methods | Summarizing peak sets |
| sparse.density | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| subsetSummary | Compute summaries for cumulative subsets of a short-read data set. |