GenomeSpy

Explore sample collections with GenomeSpy App

GenomeSpy App lets you explore genomic data from multiple samples together with sample metadata. It supports copy-number alterations, structural variants, mutations, DNA methylation, and signals from assays such as ATAC-seq and ChIP-seq. You can move from an overview of the sample collection to individual samples and genomic regions.

Samples can be filtered, grouped, and sorted using metadata or attributes derived from the genomic data—for example, copy number at a gene of interest. You can bookmark the resulting views and share them as URLs.

The App builds on GenomeSpy Core, so its views can be configured for different datasets and combinations of data types.

App documentation

Examples

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  Abstract example: Using rect and text marks to specify a labeled bar chart.
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  Abstract example: Using rect and text marks to make a labeled heatmap. The labels are automatically scaled to fit the cells. Try to zoom in and out!
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  A scatter plot with one and a half million points decorated with some annotations visualizes a miserably failed t-SNE attempt.
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  A Manhattan plot for Genome-Wide Association Study (GWAS).
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  A multiple sequence alignment that loads data from a FASTA file and displays it as a scrollable heatmap and sequence logo.
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  A structural variation visualization that uses the link mark to show arcs connecting the breakpoints. It also includes segmented copy-number data.
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  GC content of the human genome: One dataset, two visual representations. The data are loaded lazily from a BigWig file and the scale domains are autoscaled to accommodate the region.
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  Using lazy data loading, data transformations, and multiple layers to visualize the GENCODE gene annotation stored in a hierarchical GFF3 file.
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  An Observable notebook that describes how to replicate ASCAT's copy-number segmentation visualization. The visualization is interactive and thoroughly commented.
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  Exploring a sample collection with the GenomeSpy App. The visualization shows several cell-line samples with segmented copy numbers, loss of heterozygosity, and SNPs and indels.
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  GenomeSpy App visualizes ovarian high-grade serous carcinoma copy number data in the DECIDER cohort. A companion visualization for Lavikka, K., Oikkonen, J., et al. (2024) Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit. GigaScience, 13(8), giad040.
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  SegmentModel Spy. Visualizes GATK's copy-number segment models together with read and allelic counts. This is an example of using GenomeSpy as a visualization library in a special-purpose web application.