| ChIPQC-package {ChIPQC} | R Documentation |
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.
| 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.
Tom Carroll and Rory Stark
Maintainers: Tom Carroll <tc.infomatics@gmail.com> and Rory Stark <rory.stark@cruk.cam.ac.uk>
Frontiers?
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.