Genomic Data Examples

This page collects a few non-trivial genomic examples that are useful as reference material.

Linked examples

The example specs below are self-contained and focus on a single track or layout.

Chromosome Ideogram from Cytobands Shows a compact hg38 ideogram built from UCSC cytoband intervals with layered rectangles, ranged band labels, and dashed chromosome separators. RefSeq Gene Annotations with Scored Labels Shows hg38 RefSeq gene annotations with transcript bodies, exon rectangles, scored gene labels, and strand arrows that appear at detailed zoom levels. ASCAT Copy-Number Segmentation Shows simulated ASCAT sample S96 as aligned allele-specific copy-number, LogR, and B-allele-frequency tracks with segment estimates over raw probe values. ASCAT Algorithm in GenomeSpy Visualizes the ASCAT purity/ploidy fit for simulated sample S96 and shows how rounded allele-specific copy-number estimates change when rho and psi are adjusted. Sashimi Plot from Splice Junctions Recreates IGV's splice-junction demo as a lazy BigWig coverage track with dome-shaped BED splice arcs, score labels, and a minimum-read threshold control. ClinVar Small-Variant Classifications Recreates NCBI's ClinVar graphical classification view for small variants in a DSG2 region, using genomic position, row placement, and color to show germline classifications. GENCODE Gene Annotations from GFF3 Displays GENCODE release 43 transcript annotations from a tabix-indexed GFF3 file with packed transcript lanes, exons, UTR/CDS intervals, and transcript labels. Indexed FASTA Sequence Track Shows reference bases from an indexed UCSC hg38 FASTA by loading visible sequence chunks, splitting them into base-level rows, and drawing colored nucleotide labels.

More examples

For many more examples of visualizing genomic data, see Lazy data sources.

Observable notebooks

The Annotation Tracks notebook explains how to implement a chromosome ideogram and a gene annotation track.

Website examples

The genomespy.app main page showcases several examples, some of which focus on genomic data.

• GWAS Manhattan Plot (spec)
• Multiple-Sequence Alignment (spec)
• Structural Variants (spec)
• Multiple Cell Lines (spec)