damidBind

damidBind provides a formal analysis pipeline to analyse and explore differential DamID binding, gene transcription or chromatin accessibility between two conditions.

Key Features:

• Data Import: Imports processed DamID-seq data as external binding bedGraphs and GFF/BED peak calls, or as internal lists of GRanges objects.
• Peak Processing: Optionally normalises data, combines peaks across replicates, and determines per-replicate peak occupancy.
• Gene Linkage: Links bound loci to nearby genes.
• RNA Polymerase DamID Analysis: Calculates occupancy over genes and optionally calculates the FDR of significantly-enriched gene occupancy.
• Differential Analysis: Uses limma for conventional log2 ratio DamID binding data or NOIseq for counts-based CATaDa chromatin accessibility data to identify differentially-enriched regions or differentially expressed genes between two conditions.
• Visualisation: Generates volcano plots, Gene Ontology enrichment plots via ClusterProfiler, and proportional Venn diagrams via BioVenn.

Scientific Applications:

• Differential Binding Analysis: Identifies differentially-enriched DamID binding regions between two conditions using limma.
• Chromatin Accessibility Analysis: Identifies differentially-accessible chromatin regions from counts-based CATaDa data using NOIseq.
• Gene Expression Analysis: Identifies differentially expressed genes between two conditions from RNA Polymerase DamID data.
• Genomic Context Assessment: Enables assessment of significant differentially-bound regions in their genomic context through an interactive IGV genome browser interface powered by Shiny and igvShiny.

Methodology:

The pipeline imports processed DamID-seq data, optionally normalises data, combines peaks across replicates, determines per-replicate peak occupancy, links bound loci to nearby genes, and applies limma or NOIseq for differential analysis depending on data type.