wiggleplotr

wiggleplotr visualizes RNA-seq read coverage across annotated exons and rescales long introns to a fixed length to improve clarity of exon-level coverage.

Key Features:

• Exon coverage visualization: Displays RNA-seq read coverage across annotated exons to highlight exon-level expression patterns.
• Intron rescaling: Rescales introns of long transcripts to a fixed length to reduce visual distortion and emphasize exonic regions.
• Support for analyses of transcript structure variation: Produces visualizations suitable for examining alternative promoter usage and 3' untranslated region (UTR) variation.

Scientific Applications:

• Differential expression and splicing visualization: Facilitates inspection of exon-level differences relevant to differential gene expression and alternative splicing studies.
• Comparative macrophage transcriptomics: Enables visualization of transcript coverage differences between macrophages differentiated from human induced pluripotent stem cells (IPSDMs) and monocyte-derived macrophages (MDMs).
• Regulatory variation analysis: Supports investigation of alternative promoter usage and 3' UTR variations that affect gene regulation.
• Stimulus-response and functional genomics: Aids examination of transcriptomic responses to stimuli such as lipopolysaccharide (LPS) and of genes involved in chemokine signaling, antigen presentation, and tissue remodeling.

Methodology:

Processes RNA-seq read coverage to compute exon-level coverage and rescales introns of long transcripts to a fixed length for plotting.