ChIPQC-package: ChIPQC - Quality metrics for ChIPseq data

In ChIPQC: Quality metrics for ChIPseq data

Description

ChIPQC analyzes aligned reads (in .bam format) for ChIP-seq samples and their associated controls, computing a variety of quality control metrics and statistics, and providing reporting and plotting functions to enable assessment of experimental data for further analysis.

Details

Package:	ChIPQC
Type:	Package
Version:	0.1
Date:	2014-03-01
License:	GPL3

ChIPQC primarily uses two object classes: ChIPQCsample, which encapsulates the information about individual samples, and ChIPQCexperiment, which encapsulates information about larger ChIP-seq experiments (consisting of a number of samples). The primary entry point is the constructor function ChIPQC, which takes a description of an entire experiment, constructs objects for all the samples, and computes the quality metrics.

Author(s)

Tom Carroll and Rory Stark

Maintainers: Tom Carroll <[e-mail]> and Rory Stark <[e-mail]>

References

Frontiers?

See Also

ChIPQC is designed to work closely with the DiffBind package, which provides functionality for analyzing ChIP-seq experiments, including performing differential binding analysis to identify significantly differentially bound peaks.

ChIPQC documentation built on Nov. 8, 2020, 8:06 p.m.