What problem does it solve? Genomics researchers need to visualize RNA-seq, ChIP, and ATAC signal over genomic regions, but each visualization tool (UCSC exports, IGV sessions, pyGenomeTracks, igv.js) has its own format quirks and silent failure modes that waste hours of debugging. ## Core Features & Use Cases - UCSC Export Analysis: Load gzip-compressed UCSC Genome Browser JSON exports and compute signal across BED12 blocks (e.g., exons of splice isoforms) with genometracks_utils, returning tidy DataFrames and plots. - IGV Session XML Generation: Create IGV session files with correct SAMBA-mounted paths, standard hg38 annotation tracks, panel layout rules, and strand-specific coloring for local IGV viewing. - Self-Contained igv.js Notebooks: Embed fully interactive genome browsers in Quarto notebooks using gzip+base64 bedgraph data URIs, with recipes for multi-locus dropdowns, per-feature coloring, ROI highlighting, and autoscale toggles. - Use Case: Compare RNA-seq coverage across splice isoforms of a gene by exporting UCSC tracks, intersecting with a BED12 of transcript exons, and producing a weighted-mean signal table plus a publication-quality PDF plot. ## Quick Start Ask the assistant to plot bigWig signal over a genomic region or transcript set, for example: visualize RNA-seq coverage for my samples across the exons in transcripts.bed and save the figure as a PDF.
