# Differential Binding Analysis of ChIP-Seq Peak Data

## Documentation for package ‘DiffBind’ version 2.16.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DiffBind-package | Differential Binding Analysis of ChIP-seq peaksets
DBA | Standard S3 methods for DBA object
dba | Construct a DBA object
dba.analyze | Perform differential binding affinity analysis
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.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.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
DBA_ALL_ATTRIBUTES | Constant variables used in DiffBind package
DBA_ALL_BLOCK | Constant variables used in DiffBind package
DBA_ALL_METHODS | Constant variables used in DiffBind package
DBA_ALL_METHODS_BLOCK | Constant variables used in DiffBind package
DBA_CALLER | Constant variables used in DiffBind package
DBA_CONDITION | Constant variables used in DiffBind package
DBA_CONSENSUS | Constant variables used in DiffBind package
DBA_CONTROL | Constant variables used in DiffBind package
DBA_COR | Constant variables used in DiffBind package
DBA_DATA_DBAOBJECT | Constant variables used in DiffBind package
DBA_DATA_FRAME | Constant variables used in DiffBind package
DBA_DATA_GRANGES | Constant variables used in DiffBind package
DBA_DATA_RANGEDDATA | Constant variables used in DiffBind package
DBA_DATA_SUMMARIZED_EXPERIMENT | Constant variables used in DiffBind package
DBA_DESEQ | Constant variables used in DiffBind package
DBA_DESEQ2 | Constant variables used in DiffBind package
DBA_DESEQ2_BLOCK | Constant variables used in DiffBind package
DBA_DESEQ_BLOCK | Constant variables used in DiffBind package
DBA_DESEQ_CLASSIC | Constant variables used in DiffBind package
DBA_DESEQ_GLM | Constant variables used in DiffBind package
DBA_EDGER | Constant variables used in DiffBind package
DBA_EDGER_BLOCK | Constant variables used in DiffBind package
DBA_EDGER_CLASSIC | Constant variables used in DiffBind package
DBA_EDGER_GLM | Constant variables used in DiffBind package
DBA_FACTOR | Constant variables used in DiffBind package
DBA_FRIP | Constant variables used in DiffBind package
DBA_GROUP | Constant variables used in DiffBind package
DBA_ID | Constant variables used in DiffBind package
DBA_INALL | Constant variables used in DiffBind package
DBA_INTERVALS | Constant variables used in DiffBind package
DBA_OLAP | Constant variables used in DiffBind package
DBA_OLAP_ALL | Constant variables used in DiffBind package
DBA_OLAP_PEAKS | Constant variables used in DiffBind package
DBA_OLAP_RATE | Constant variables used in DiffBind package
DBA_READS_BAM | Constant variables used in DiffBind package
DBA_READS_BED | Constant variables used in DiffBind package
DBA_READS_DEFAULT | Constant variables used in DiffBind package
DBA_REPLICATE | Constant variables used in DiffBind package
DBA_SCORE_READS | Constant variables used in DiffBind package
DBA_SCORE_READS_FOLD | Constant variables used in DiffBind package
DBA_SCORE_READS_MINUS | Constant variables used in DiffBind package
DBA_SCORE_RPKM | Constant variables used in DiffBind package
DBA_SCORE_RPKM_FOLD | Constant variables used in DiffBind package
DBA_SCORE_SUMMIT | Constant variables used in DiffBind package
DBA_SCORE_SUMMIT_ADJ | Constant variables used in DiffBind package
DBA_SCORE_SUMMIT_POS | Constant variables used in DiffBind package
DBA_SCORE_TMM_MINUS_EFFECTIVE | Constant variables used in DiffBind package
DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM | Constant variables used in DiffBind package
DBA_SCORE_TMM_MINUS_FULL | Constant variables used in DiffBind package
DBA_SCORE_TMM_MINUS_FULL_CPM | Constant variables used in DiffBind package
DBA_SCORE_TMM_READS_EFFECTIVE | Constant variables used in DiffBind package
DBA_SCORE_TMM_READS_EFFECTIVE_CPM | Constant variables used in DiffBind package
DBA_SCORE_TMM_READS_FULL | Constant variables used in DiffBind package
DBA_SCORE_TMM_READS_FULL_CPM | Constant variables used in DiffBind package
DBA_TISSUE | Constant variables used in DiffBind package
DBA_TREATMENT | Constant variables used in DiffBind package
DiffBind | Differential Binding Analysis of ChIP-seq peaksets
plot.DBA | Standard S3 methods for DBA object
print.DBA | Standard S3 methods for DBA object
summary.DBA | Standard S3 methods for DBA object
tamoxifen | Tamoxifen resistance dataset used for DBA examples
tamoxifen_analysis | Tamoxifen resistance dataset used for DBA examples
tamoxifen_counts | Tamoxifen resistance dataset used for DBA examples
tamoxifen_peaks | Tamoxifen resistance dataset used for DBA examples