chipseq v1.22.0

chipseq: A package for analyzing chipseq data

Tools for helping process short read data for chipseq experiments

Functions in chipseq

Name Description
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.
subsetSummary Compute summaries for cumulative subsets of a short-read data set.
peakCutoff Calculate a peak cutoff
islandDepthPlot Plot island depth distribution
laneSubsample Subsample short read alignment locations
cstest A test ChIP-Seq dataset
chipseqFilter Filtering ChIP-seq reads
peakSummary-methods Summarizing peak sets
diffPeakSummary A function to identify and produce summary statistics for differentially expressed peaks.
coverageplot Plot coverage on a small interval.
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