ChIPQC (version 1.8.2)

ChIPQC-package: 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.

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.