Differential Binding Analysis of ChIP-Seq peak data


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Documentation for package ‘DiffBind’ version 2.0.9

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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.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