Differential Binding and Expression Analysis for DamID-seq Data

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Documentation for package ‘damidBind’ version 0.99.12

• 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