Kari Lavikka
@karilavikka.fi
Researcher working on bioinformatics, WebGL-powered cancer genome visualization, and tumor evolution.
Reposted by Kari Lavikka
💥 First #BioVis meetup of 2026 💥
#DataVis
“Crafting visual biomedical stories“ with Laura Garrison, University of Bergen
- Virtual, no registration, link/more info:
biovis.net/2026/meetup/...
- Wednesday, 21. January, 5pm Berlin/4pm London
#DataVis
“Crafting visual biomedical stories“ with Laura Garrison, University of Bergen
- Virtual, no registration, link/more info:
biovis.net/2026/meetup/...
- Wednesday, 21. January, 5pm Berlin/4pm London
BioVis Meetup #12: Crafting visual biomedical stories
Title: Crafting visual biomedical stories
biovis.net
January 21, 2026 at 3:02 PM
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 🤷
June 23, 2025 at 4:09 PM
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 🤷
Reposted by Kari Lavikka
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)
June 17, 2025 at 4:43 PM
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)
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. ❤️
April 30, 2025 at 12:07 PM
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. ❤️
Jellyfish visualization tool and the Jellyfisher R package have now been published in OUP Bioinformatics! 🎉 doi.org/10.1093/bioi... #Bioinformatics #DataViz (1/7)
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
doi.org
February 26, 2025 at 1:52 PM
Jellyfish visualization tool and the Jellyfisher R package have now been published in OUP Bioinformatics! 🎉 doi.org/10.1093/bioi... #Bioinformatics #DataViz (1/7)
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....
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...
cran.r-project.org
February 7, 2025 at 12:49 PM
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....
Reposted by Kari Lavikka
🚨 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/
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/
August 22, 2024 at 10:08 AM
🚨 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/
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/
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.
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
academic.oup.com
August 6, 2024 at 9:35 AM
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.