Learn R Programming

DiffBind (version 2.0.2)

Differential Binding Analysis of ChIP-Seq peak data

Description

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

Copy Link

Version

Version

2.0.2

License

Artistic-2.0

Maintainer

Rory Stark

Last Published

February 15th, 2017

Functions in DiffBind (2.0.2)

DiffBind-package

Differential Binding Analysis of ChIP-seq peaksets
dba.contrast

Set up contrasts for differential binding affinity analysis
dba.mask

Derive a mask to define a subset of peaksets or sites for a DBA object
dba.plotHeatmap

Draw a binding site heatmap
dba.plotBox

Boxplots
dba.plotPCA

PCA plot
dba.save

save DBA object
dba.plotVenn

Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps
DiffBind -- DBA global constant variables

Constant variables used in DiffBind package
dba.show

List attributes of peaksets of contrasts associated with a DBA object
DBA object methods

Standard S3 methods for DBA object
dba.plotMA

Generate MA and scatter plots of differential binding analysis results
dba.peakset

Add a peakset to, or retrieve a peakset from, a DBA object
dba.report

Generate a report for a differential binding affinity analysis
dba.count

Count reads in binding site intervals
dba.overlap

Compute binding site overlaps (occupancy analysis)
dba.load

load DBA object
DBA tamoxifen resistance dataset

Tamoxifen resistance dataset used for DBA examples
dba.analyze

Perform differential binding affinity analysis
dba

Construct a DBA object