# Differential Binding and Expression Analysis for DamID-seq Data

## Documentation for package ‘damidBind’ version 1.0.0

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

## Help Pages

analyse_go_enrichment | Perform Gene Ontology (GO) enrichment analysis for differentially bound/expressed regions
analysisTable | Access the differential binding analysis results
analysisTable-method | Access the differential binding analysis results
analyze_go_enrichment | Perform Gene Ontology (GO) enrichment analysis for differentially bound/expressed regions
browse_igv_regions | Interactive IGV visualisation (Shiny + igvShiny) of differential regions
calculate_and_add_occupancy_pvals | Calculate and add gene occupancy FDR
calculate_occupancy | Compute occupancy for genomic regions
conditionNames | Access condition name mapping
conditionNames-method | Access condition name mapping
DamIDResults | The DamIDResults Class
DamIDResults-class | The DamIDResults Class
differential_accessibility | Differential accessibility analysis for CATaDa ('NOISeq' based)
differential_binding | Differential binding/expression analysis ('limma')
enrichedCond1 | Access Condition 1 enriched regions
enrichedCond1-method | Access Condition 1 enriched regions
enrichedCond2 | Access Condition 2 enriched regions
enrichedCond2-method | Access Condition 2 enriched regions
expressed | Get expressed genes/loci by FDR
expressed-method | Get expressed genes/loci by FDR
extract_unique_sample_ids | Extract unique sample names from complex labels
filter_genes_by_fdr | Filter genes by FDR within a specific condition
get_ensdb_genes | Extract gene annotation from Ensembl via AnnotationHub EnsDb
inputData | Access original input data and metadata
inputData-method | Access original input data and metadata
load_data_genes | Load genome-wide binding data for gene expression (RNA polymerase occupancy)
load_data_peaks | Load genome-wide binding data and associated peak files or GRanges objects
plot_input_diagnostics | Display diagnostic plots for input data
plot_limma_diagnostics | Verify Underlying Assumptions for 'limma' Analysis
plot_venn | Draw proportional Venn diagrams for differential binding analysis
plot_volcano | Volcano plot of differentially bound/expressed loci
quantile_normalisation | Quantile normalisation (native R code version)
quantile_normalization | Quantile normalisation (native R code version)
reduce_regions | Reduce a list of GRanges to unique, non-overlapping regions
sample_labels_by_isolation | Sample data points based on local isolation