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Kari Lavikka

@karilavikka.fi

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

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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Reposted by Kari Lavikka

Helena Klara Jambor @helenajambor.bsky.social · 21/01/2026

see you in 1 hour! #BioVis #DataVis meetup

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Kari Lavikka @karilavikka.fi · 23/06/2025

Parquet and Arrow are great columnar formats, but the abysmal performance of TextDecoder on Chrome (or maybe V8) completely kills any speed benefits when files contain lots of short, unique strings. Even #JavaScript CSV parsers are faster. It’s fine if you don’t need to access the string columns 🤷

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Reposted by Kari Lavikka

Alex Russell @infrequently.org · 20/06/2025

Checks out: www.jonoalderson.com/conjecture/j...

jonoalderson.com

JavaScript broke the web (and called it progress)

We replaced simple websites with complex apps nobody asked for. Now it takes a complex build pipeline just to change a headline.

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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 · 30/04/2025

I've typically used R (with tidyverse) for analyses, but recently I've been familiarizing myself with Python. Pandas feels quite awkward to me, at least compared to dplyr. But @pola.rs is great! It works wonderfully with Parquet files too. ❤️

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

Jellyfish visualization tool and the Jellyfisher R package have now been published in OUP Bioinformatics! 🎉 doi.org/10.1093/bioi... #Bioinformatics #DataViz (1/7)

doi.org

Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics

AbstractSummary. Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to c

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Kari Lavikka @karilavikka.fi · 07/02/2025

Thrilled to announce that my R package 'jellyfisher' is now available on CRAN! It's my first package submission to CRAN, and a related paper will (hopefully) be published soon. Check it out: cran.r-project.org/web/packages....

cran.r-project.org

jellyfisher: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots

Generates interactive Jellyfish plots to visualize spatiotemporal tumor evolution by integrating sample and phylogenetic trees into a unified plot. This approach provides an intuitive way to analyze t...

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Reposted by Kari Lavikka

Helena Klara Jambor @helenajambor.bsky.social · 22/08/2024

🚨 next #BioVis #Dataviz virtual meetup: Will Stahl-Timmins (The #BMJ) is joining us on Sept 18! "A picture of health: Visualisations in medical publishing" Details & Link: biovis.net/2024/meetup/

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Kari Lavikka @karilavikka.fi · 06/08/2024

My first first-author paper is now published: doi.org/10.1093/giga.... GenomeSpy is a grammar-based visualization toolkit for genomic data, powered by efficient WebGL rendering. Check the paper for examples on how we use it to explore a large ovarian high-grade serous carcinoma dataset.

academic.oup.com

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

AbstractBackground. Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remai

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