Package index
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DamIDResults-classDamIDResults - The DamIDResults Class
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analyse_go_enrichment() - Perform Gene Ontology (GO) enrichment analysis for differentially bound/expressed regions
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analysisTable() - Access the differential binding analysis results
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browse_igv_regions() - Interactive IGV visualisation (Shiny + igvShiny) of differential regions
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calculate_and_add_fdr() - Calculate and add gene occupancy FDR
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calculate_occupancy() - Compute occupancy for genomic regions
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conditionNames() - Access condition name mapping
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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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enrichedCond1() - Access Condition 1 enriched regions
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enrichedCond2() - Access Condition 2 enriched regions
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expressed() - Get expressed genes/loci by FDR
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filter_genes_by_fdr() - Filter genes by FDR within a specific condition
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get_ensdb_genes() - Extract gene annotation from Ensembl via AnnotationHub EnsDb
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inputData() - Access original input data and metadata
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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 diagrams 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 (native R code version)
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reduce_regions() - Reduce a list of GRanges to unique, non-overlapping regions
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sample_labels_by_isolation() - Sample data points based on local isolation