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 3.2.7 Index]