I use Quarto to build interactive #dataviz with Observable #javascript to explore data of article processing charges in academic publishing. Explore the data for yourself: jefworks.github.io/APC_quarto/ #DataAnalytics #AcademicTwitter #AcademicChatter #AcademicPublishing

Has the scientific literature been flooded w/ papers containing #AI-generated text? I use #rstats to scrape Google Scholar to count the # of pubs w/ #LLM-generated phrases over time (compared to other phrases) 👉 jef.works/blog/2024/03/1… #AcademicTwitter #codetutorial #dataviz

In this #bioinformatics #codingtutorial, I quickly identify spatially variable genes in a #singlecell #spatialtranscriptomic dataset w/ 377,985 cells by combining our recent preprocessing tool SEraster with MERINGUE in #Rstats. Try it out for yourself: jef.works/blog/2024/03/2…

Just finished teaching another semester of genomic #datavisualization 🥳 Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data Check out the course notes + #Rstats code to explore for yourself: jef.works/genomic-data-v…

In this blog post, I show how although we developed STalign to structurally align #spatialtranscriptomics data, we can use the same tool + underlying math to align tissue images at #singlecell resolution Try it out: jef.works/blog/2024/04/1… #bioinformatics #Python #codetutorial

I use #rstats to shop for medical services by analyzing CMSGov Hospital Price Transparency data to compare prices at 3 hospitals near me. Check out the #codetutorial + apply what you learn to the hospitals near you: jef.works/blog/2024/04/2… #MedTwitter #healthcare #dataviz

As the encampment here at Hopkins comes to a peaceful resolution, I wanted to provide a snapshot of my evolving thoughts and document the events around me through this written reflection and short film: What is a university and who should it serve?youtube.com/watch?v=YfisDY…

Our paper characterizing the impact of different #geneexpression normalization with different gene panels in analysis + interpretation of #singlecell imaging-based targeted #spatialtranscriptomics data is now out Genome Biology Summary and 🧵👇 Congrats to Lyla Atta + team 🥂

I've encountered papers with 'data available upon request' and 'code available upon request' but 'results available upon request'? So ridiculous I made a comedic short about it 🤣 youtube.com/shorts/Sfs-xCo… Additional rants available upon request #AcademicTwitter #PhDLife

I made a fashion ad for luxury goods (academic edition) 🤣📽️ youtube.com/shorts/is3Anxd… #AcademicTwitter #PhDLife It can cost >$10k to publish in Nature yet some of their current editors/staff have been forced to strike for fair pay: chemistryworld.com/news/springer-… #springernaturestrike

I use #ggplot2 #gganimate in to create an animation of #july4 fireworks w/ a background image in #Rstats. Had to brush up on polar coordinates 😅 Check out the code #gist + try it out for yourself: gist.github.com/JEFworks/c59b8… #HappyFourth 🥳 #artwithcode #dataviz #creativecoding

I was able to use the gm package in #RStats to quickly see how the intro to Stairway to Heaven sounded with different instruments. Harp is so far my favorite so far. What do you think? Try it out for yourself: gist.github.com/JEFworks/d7a9e… #creativecoding #funwithcode

Check out our just published SEraster tool for aggregating #SingleCell #SpatialTranscriptomics data into square/hex pixels for scalable spatial #DataAnalysis. Paper: academic.oup.com/bioinformatics… Software: github.com/JEFworks-Lab/S… #RStats Congrats to Gohta Aihara + team 🥂 See 🧵👇

In this blog post, I use our recent SEraster #Rstats tool to perform spatial bootstrapping to evaluate the stability of cell-type proportion estimates from #singlecell #spatialtranscriptomics data. Try it out for yourself: jef.works/blog/2024/07/2… #bioinformatics #codetutorial

Learning how to share my scientific talks from home (v5) In this abbreviated talk, I discuss considerations for #geneexpression count normalization in #singlecell imaging-based #spatiallytranscriptomics 📽️: youtu.be/phzYB9rmcEg?si… #bioinformatics #dataanalysis #AcademicTwitter

In this blog post, I compare 4 implementations of Moran's I in #Rstats to identify SVGS in #spatialtranscriptomics data. I show how they vary in runtime + caution that some only allow two-sided tests, leading to incorrect SVGs. Code along: jef.works/blog/2024/08/2… #CodingTutorial