| 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 |