chipseq: A package for analyzing chipseq data

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Documentation for package ‘chipseq’ version 1.56.0

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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.