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chipseq (version 1.22.0)

chipseq: A package for analyzing chipseq data

Description

Tools for helping process short read data for chipseq experiments

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Version

Version

1.22.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in chipseq (1.22.0)

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.