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Kari Lavikka

@karilavikka.fi

Researcher working on bioinformatics, WebGL-powered cancer genome visualization, and tumor evolution.

Kari Lavikka @karilavikka.fi · 01/10/2026

I made a bold move: I bumped the GenomeSpy version from v0.90.0 to … v1.0.0! 🎉 I also wrote a blog post about it, reflecting a bit on the development journey: genomespy.app/blog/posts/2...

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Kari Lavikka @karilavikka.fi · 26/08/2026

I made an R package that creates oncoplots, lollipop plots, rainfall plots, and GISTIC plots with basic interactivity such as tooltips and zooming. It's almost a drop-in replacement for the corresponding maftools' plotting functions.

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Kari Lavikka @karilavikka.fi · 04/08/2026

When doing copy-number analysis, have you ever struggled to interpret ASCAT sunrise plots and similar purity/ploidy grids? Have you wanted to compare how different solutions affect the allele-specific copy-number fit and better understand the fitting procedure?

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Kari Lavikka @karilavikka.fi · 28/07/2026

I recently added a parameterizable arrow mark to GenomeSpy, my open-source toolkit for interactive genomic data visualization, and implemented a couple of fancy examples to showcase it. (1/3)

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Kari Lavikka @karilavikka.fi · 17/06/2025

Selections can also drive filtering and aggregation, though the code is still entirely CPU-based for now. I’d like to explore columnar and GPU-based approaches in the future. (2/2)

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Kari Lavikka @karilavikka.fi · 17/06/2025

It’s been a bit quiet on the GenomeSpy front, but I finally had time to implement interval selections and other fancy features. Vega-Lite–style conditional encodings are compiled into shader code, with selection tests running on the GPU—making interactions snappy. (1/2)

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Kari Lavikka @karilavikka.fi · 26/02/2025

Metastases in solid tumors consist of heterogeneous subclonal mixtures that evolve across space and time. Jellyfish integrates tumor phylogeny and subclonal compositions of spatiotemporal samples into a unified plot, making subclonal dynamics easier to interpret. #CancerResearch (2/7)

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