Examples¶

This page collects non-trivial examples that are useful as reference material and demonstrate the capabilities of GenomeSpy.

Genomic data examples¶

The example specs below mostly display a single dataset to keep the examples simple and focused. Gene annotation track, etc. are omitted from the examples.

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.

Interactive ASCAT-like Purity/Ploidy Fitting Visualizes ASCAT purity/ploidy fits for simulated samples and shows how rounded allele-specific copy-number estimates change when rho and psi are adjusted.

HCC1954 Structural Variants and Copy Number Shows paired Severus somatic SV arcs and Wakhan ploidy-relative copy-number segments for the highly rearranged HCC1954 breast-cancer cell line.

TCGA Ovarian Cancer GISTIC2 Copy-Number Landscape Shows recurrent GISTIC2 copy-number amplifications and deletions across the TCGA ovarian serous cystadenocarcinoma cohort.

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 Six-Frame Translation Translates a visible hg38 FASTA interval in three forward and three reverse reading frames using generic flattenSequence, lookup, window, and formula transforms.

BAM Read Alignments Shows an IGV-like BAM alignment view with depth coverage, insertion and mismatch summaries, directional read pileups, CIGAR overlays, and base-quality filtering.

Multiple Sequence Alignment Visualizes the 16SRNA_Deino_87seq nucleotide alignment with a sequence logo showing per-position information content and a zoomable base-by-base alignment.

SPI1 Binding-QTL Dynseq Track Compares per-base projected DeepSHAP contribution scores for the reference C and alternate G alleles of rs5764238 in GM12878 SPI1 ChIP-seq BPNet predictions.

Composing a Genome Browser Combines existing visualizations into a genome-browser-like view with multiple tracks sharing the x-axis.

Generic visualization examples¶

Set Intersections with an UpSet Plot Shows exact mutation intersections among five genes in a glioblastoma cohort using aligned set-size bars, intersection-size bars, and hover-linked matrix highlighting.

More examples¶

For 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.