DiffBind-package {DiffBind}R Documentation

Differential Binding Analysis of ChIP-seq peaksets

Description

Differential binding analysis of ChIP-seq peaksets

Details

Computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Entry Points:

dba: Construct a dba object
dba.peakset: Add a peakset to, or retrieve a peakset from, a dba object
dba.overlap: Compute binding site overlaps and/or correlations
dba.blacklist: Filter peaks using blacklists and greylists
dba.count: Count reads in binding sites
dba.contrast: Establish design and contrast(s) for analysis
dba.normalize: Normalize count data for analysis
dba.analyze: Execute quantitative analysis
dba.report: Generate results report for a contrast analysis
dba.plotHeatmap: Heatmap plot
dba.plotPCA: Principal Components plot
dba.plotBox: Boxplots
dba.plotMA: MA/scatter plot
dba.plotVenn: Venn diagram plot
dba.plotVolcano: Volcano plot
dba.plotProfile: Peak profile heatmaps
dba.show: Show dba metadata
dba.mask: Mask samples or sites
dba.save: Save dba object
dba.load: Load dba object

Author(s)

Rory Stark <rory.stark @at@ cruk.cam.ac.uk> and Gord Brown <gdbzork @at@ gmail.com>


[Package DiffBind version 3.3.4 Index]