ChIPQC-package: ChIPQC - Quality metrics for ChIPseq data

ChIPQC-packageR Documentation

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 <tc.infomatics@gmail.com> and Rory Stark <rory.stark@cruk.cam.ac.uk>

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.


shengqh/ChIPQC documentation built on Feb. 27, 2023, 10:51 p.m.