Differential Binding Analysis of ChIP-seq peaksets


Differential binding analysis of ChIP-seq peaksets


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.count: Count reads in binding sites
dba.contrast: Establish contrast(s) for analysis
dba.analyze: Execute affinity analysis
dba.report: Generate 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.show: Show dba metadata
dba.mask: Mask samples or sites
dba.save: Save dba object
dba.load: Load dba object


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

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