# chipseq: A package for analyzing chipseq data

## Documentation for package ‘chipseq’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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.
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.