DBA-object              Standard S3 methods for DBA object
DBA_ID                  Constant variables used in DiffBind package
DiffBind-package        Differential Binding Analysis of ChIP-seq
                        peaksets
DiffBind3               Differences between DiffBind 3.0 and earlier
                        versions
dba                     Construct a DBA object
dba.analyze             Perform differential binding affinity analysis
dba.blacklist           Apply blacklists and/or greylists to peaks (and
                        generate greylist)
dba.contrast            Set up contrasts for differential binding
                        affinity analysis
dba.count               Count reads in binding site intervals
dba.load                load DBA object
dba.mask                Derive a mask to define a subset of peaksets or
                        sites for a DBA object
dba.normalize           Specify parameters for normalizing a dataset;
                        calculate library sizes and normalization
                        factors.
dba.overlap             Compute binding site overlaps (occupancy
                        analysis)
dba.peakset             Add a peakset to, or retrieve a peakset from, a
                        DBA object
dba.plotBox             Boxplots
dba.plotHeatmap         Draw a binding site heatmap
dba.plotMA              Generate MA and scatter plots of differential
                        binding analysis results
dba.plotPCA             PCA plot
dba.plotProfile         Generate profiles and make profile heatmaps
dba.plotVenn            Draw 2-way, 3-way, or 4-way Venn diagrams of
                        overlaps
dba.plotVolcano         Generate volcano plots of differential binding
                        analysis results
dba.report              Generate a report for a differential binding
                        affinity analysis
dba.save                save DBA object
dba.show                List attributes of peaksets of contrasts
                        associated with a DBA object
tamoxifen               Tamoxifen resistance dataset used for DBA
                        examples
