R: Differential Binding Analysis of ChIP-Seq Peak Data

# Differential Binding Analysis of ChIP-Seq Peak Data

## Documentation for package ‘DiffBind’ version 3.22.2

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

## Help Pages

D P S T

DiffBind-package | Differential Binding Analysis of ChIP-seq peaksets

## -- D --

dba | Construct a DBA object
DBA-config | Standard S3 methods for DBA object
DBA-object | Standard S3 methods for DBA object
dba.analyze | Perform differential binding affinity analysis
dba.blacklist | Apply blacklists and/or greylists to peaks (and generate greylist)
DBA.config | Standard S3 methods for DBA object
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.object | Standard S3 methods for 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.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
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_BLACKLIST | Constant variables used in DiffBind package
DBA_BLACKLISTED_PEAKS | Constant variables used in DiffBind package
DBA_BLACKLIST_CE10 | Constant variables used in DiffBind package
DBA_BLACKLIST_CE11 | Constant variables used in DiffBind package
DBA_BLACKLIST_DM3 | Constant variables used in DiffBind package
DBA_BLACKLIST_DM6 | Constant variables used in DiffBind package
DBA_BLACKLIST_GRCH37 | Constant variables used in DiffBind package
DBA_BLACKLIST_GRCH38 | Constant variables used in DiffBind package
DBA_BLACKLIST_HG19 | Constant variables used in DiffBind package
DBA_BLACKLIST_HG38 | Constant variables used in DiffBind package
DBA_BLACKLIST_MM10 | Constant variables used in DiffBind package
DBA_BLACKLIST_MM9 | 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_DESEQ2 | Constant variables used in DiffBind package
DBA_DESEQ2_BLOCK | 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_GLM | Constant variables used in DiffBind package
DBA_FACTOR | Constant variables used in DiffBind package
DBA_FRIP | Constant variables used in DiffBind package
DBA_GREYLIST | 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_LIBSIZE_BACKGROUND | Constant variables used in DiffBind package
DBA_LIBSIZE_DEFAULT | Constant variables used in DiffBind package
DBA_LIBSIZE_FULL | Constant variables used in DiffBind package
DBA_LIBSIZE_PEAKREADS | Constant variables used in DiffBind package
DBA_LIBSIZE_USER | Constant variables used in DiffBind package
DBA_NORM_DEFAULT | Constant variables used in DiffBind package
DBA_NORM_LIB | Constant variables used in DiffBind package
DBA_NORM_NATIVE | Constant variables used in DiffBind package
DBA_NORM_OFFSETS | Constant variables used in DiffBind package
DBA_NORM_OFFSETS_ADJUST | Constant variables used in DiffBind package
DBA_NORM_RLE | Constant variables used in DiffBind package
DBA_NORM_SPIKEIN | Constant variables used in DiffBind package
DBA_NORM_TMM | Constant variables used in DiffBind package
DBA_NORM_USER | Constant variables used in DiffBind package
DBA_OFFSETS_LOESS | Constant variables used in DiffBind package
DBA_OFFSETS_USER | 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 | 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_CONCENTRATION | Constant variables used in DiffBind package
DBA_SCORE_CONC_DENOMINATOR | Constant variables used in DiffBind package
DBA_SCORE_CONC_NUMERATOR | Constant variables used in DiffBind package
DBA_SCORE_CONTROL_READS | Constant variables used in DiffBind package
DBA_SCORE_FDR | Constant variables used in DiffBind package
DBA_SCORE_FOLD | Constant variables used in DiffBind package
DBA_SCORE_NORMALIZED | Constant variables used in DiffBind package
DBA_SCORE_PVAL | Constant variables used in DiffBind package
DBA_SCORE_READS | Constant variables used in DiffBind package
DBA_SCORE_READS_EFFECTIVE | Constant variables used in DiffBind package
DBA_SCORE_READS_FOLD | Constant variables used in DiffBind package
DBA_SCORE_READS_FULL | Constant variables used in DiffBind package
DBA_SCORE_READS_MINUS | Constant variables used in DiffBind package
DBA_SCORE_READS_MINUS_EFFECTIVE | Constant variables used in DiffBind package
DBA_SCORE_READS_MINUS_FULL | 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_RPKM_MINUS | 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
DiffBind-config | Standard S3 methods for DBA object
DiffBind.config | Standard S3 methods for DBA object
DiffBind3 | Differences between DiffBind 3.0 and earlier versions

## -- P --

plot.DBA | Standard S3 methods for DBA object
print.DBA | Standard S3 methods for DBA object

## -- S --

summary.DBA | Standard S3 methods for DBA object

## -- T --

tamoxifen | Tamoxifen resistance dataset used for DBA examples
tamoxifen.greylist | 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_greylist | Tamoxifen resistance dataset used for DBA examples
tamoxifen_peaks | Tamoxifen resistance dataset used for DBA examples