Package index
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show(<DamIDResults>)analysisTable()enrichedCond1()enrichedCond2()conditionNames()plot(<DamIDResults>,<missing>) - The DamIDResults Class
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all_overlaps_to_original() - Find best gene overlap(s) for each query interval
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analyse_go_enrichment() - Perform Gene Ontology (GO) Enrichment Analysis for Differentially Bound/Expressed Regions
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browse_igv_regions() - Interactive IGV visualisation (Shiny + igvShiny) of differential regions
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differential_accessibility() - Differential Accessibility Analysis for CATaDa (NOISeq based)
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differential_binding() - Differential Binding/Expression Analysis (limma)
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gene_occupancy() - Compute average occupancy for each gene, using DamID binding profiles
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get_ensdb_genes() - Extract gene annotation from Ensembl via AnnotationHub EnsDb
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gr_occupancy() - Compute occupancy (average) per region over a set of GRanges
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load_data_genes() - Load genome-wide binding data for gene expression (RNA polymerase occupancy)
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load_data_peaks() - Load genome-wide binding data and associated peak files or GRanges objects
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plot_venn() - Draw Proportional Venn Diagram for differential binding analysis
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plot_volcano() - Volcano Plot of Differentially Bound/Expressed Loci
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quantile_normalisation() - Quantile Normalisation
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reduce_regions() - Reduce a list of GRanges to unique, non-overlapping regions