* Follow @sara-altman.bsky.social and @simonpcouch.com

140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 07 summary lcolladotor.github.io/jhustatcompu... Guest speaker: @nick-eagles.bsky.social from @lieberinstitute.bsky.social #RStats #DataScience #PositAssistant #AIcoding #Claude

Woo! posit::conf(2026) started this morning, and I am super happy and grateful to be a Posit Opportunity Scholar this year! I am starting the week attending the Modern R Workflow Workshop taught by @jennybryan.bsky.social and @hadley.nz #PositConf2026

Day 1 of talks at posit::conf(2026) started with keynote speakers @sara-altman.bsky.social and @simonpcouch.com They talked about Posit’s efforts on building AI tools that are correct (trustworthy) while staying convenient (straightforward and intuitive). slides: pos.it/keynote #PositConf2026

After a few more sprints between rooms and more great talks, we finished the day with the keynote by @christinezhang.bsky.social, Graphics Editor at The NYT. She’s part of the team behind many of the graphs the NYT times used on election night in 2024. (I was fangirling cuz she is so cool 😅)

Headed to Houston for #positconf! I can’t overstate the impact that @posit.co’s opensource products & packages (RStudio, Positron, tidyverse) have had on me as a journalist & data nerd 🤓 Thrilled/terrified to be giving a keynote presentation on Tues. If you’re there, say hello! conf.posit.co/2026/

Very interesting! We looked at using perplexity to evaluate quantification estimates in the absence of a ground truth (link.springer.com/article/10.1...). Our inspiration was NLP. I think it's a potentially very useful metric overall.

Perplexity: evaluating transcript abundance estimation in the absence of ground truth - Algorithms for Molecular Biology

Background There has been rapid development of probabilistic models and inference methods for transcript abundance estimation from RNA-seq data. These models aim to accurately estimate transcript-leve...

link.springer.com

Megan D. Schertzer from @davidaknowles.bsky.social’s lab invites us to use « perplexity » from Ecology to measure isoform diversity (or other molecular units). Very thought provoking! 🤔 More at doi.org/10.1101/2025... #BoG2026 @cshlmeetings.bsky.social

Boxiang @boxiangliu.bsky.social showcased #ISAAC for computing splicing QTLs #sQTLs using single cell data They applied it to DLPFC 🧠 data from 722 donors github.com/boxiangliula... #BoG2026 @cshlmeetings.bsky.social

Brian Clearly’s work on « Fundamental errors in #RNAvelocity arising from the omission of cell growth » feels like a must read!! Brian shouted out the co-authors in the second slide 👏🏽 #BoG2026 @cshlmeetings.bsky.social doi.org/10.64898/202...

Mike @mikeschatz.bsky.social paid tribute to James P. Taylor who was one of the main champions of #OpenScience @jxtxfoundation.bsky.social carries on. Mike introduced the winners of the scholarship to attend #BoG2026 this year (sponsored by @pacbio.bsky.social this yr) 👏🏽 @cshlmeetings.bsky.social

Yoav @ygilad.bsky.social kickstarts #BoG2026 at @cshlmeetings.bsky.social by asking us to be open minded and think beyond biology defined by means. To think about the dispersion / variance.

@libdrstats.bsky.social videos and blog posts continue to be a great resource for me as I delve into snRNAseq analyses, and for lots of other bioinformatics-related topics! Learn more here: research.libd.org/rstatsclub/

LIBD rstats club

Continuous rstats learning

research.libd.org

Check out my first @libdrstats.bsky.social presentation on one strategy our team @lcolladotor.bsky.social at @lieberinstitute.bsky.social is taking to deal with doublets during quality control for single nucleus RNA-sequencing data: www.youtube.com/watch?v=SMA-...

[2026-02-27] Strategy to drop doublets during snRNAseq QC steps

YouTube video by Leonardo Collado Torres

youtube.com

Talk submission video for Posit Conf 2026 #RStats «Organizing your data science team to be efficient, adaptive to new developments, and resilient to turnover rate» URLs: 1. lcolladotor.github.io/bioc_team_ds/ 2. research.libd.org/rstatsclub/ 3. github.com/LieberInstit... #OpenSource #Bioconductor

Issue 31 of RDM Weekly is out! 📬 ➡️ OS resources in Comm Sciences @csdisseminate.bsky.social ➡️ RDA 25th Plenary Meeting Programme @researchdataall.bsky.social ➡️ Ask for R Help by Creating a Small Reproducible Example @libdrstats.bsky.social and more! rdmweekly.substack.com/p/rdm-weekly...

RDM Weekly - Issue 031

A weekly roundup of Research Data Management resources.

rdmweekly.substack.com

lcolladotor.github.io/rnaseq_LCG-U... is looking ready for next week! We'll have the most guest presenters ever this year with @meli-mq99.bsky.social @gabrielramirezv.bsky.social @mariagtac.bsky.social & @daiannaglez.bsky.social 🙌🏽 See you soon at LCG-UNAM! 🇲🇽 #RStats @bioconductor.bsky.social

In a recent journal club, I covered the SOFA paper by @wkhuber.bsky.social and colleagues. It's especially cool how you can guide the factorization approach with known covariates. Check out their preprint (doi.org/10.1101/2024...) and our discussion (youtu.be/WKs-g4lXzZs)!

A colleague Geo @geopertea.bsky.social found out a cool trick to get Positron working with full support at our computing cluster JHPCE (remote file explorer, Positron assistant seeing the remote R session). Game changer for my work at LIBD! Check out his demo video (youtu.be/CnmaJG8VPp8) #positron

@nick-eagles.bsky.social concluded that scratch space location matters significantly for performance 💾⚡. He explained his motivation: he had a real use case with hundreds of millions of rows 📊 that originally took Full length video: youtu.be/ikumz_QLZiE #RStats #dplyr #duckplyr #rpolars #data.table

@nick-eagles.bsky.social introduced his presentation on benchmarking #dplyr alternatives 📊💻. He planned to review public benchmarks of various data manipulation packages 📦 as well as his own custom benchmark results 🔬 Full length 🎥: youtu.be/ikumz_QLZiE #RStats #dplyr #duckplyr #rpolars #data.table

@geopertea.bsky.social discussed how the AI provides semantic understanding of code 🧠💻, showing how objects are generated from different parts of the codebase 🔗. He acknowledged that you can do this manually too 👨‍💻, and sometimes manual inspection might ... #RStats #PositronIDE @posit.co

@geopertea.bsky.social showed his chat history 📜 and explained a useful use case: he asked the AI to look into a repository 🔍 and tell him what methods they were using for calculations 🧮. Basically, he had the AI read the code and summarize it for him 📝✨. #RStats #Positron #PositronAI

@geopertea.bsky.social explained how you can add your own custom agents 🤖 to #Positron & showed the interactive way to configure them 🛠️. He demonstrated how the "plan" agent is defined, noting that it doesn't use any file mod tools 📝❌ - it's specifically designed for planning purposes 📋 #RStats

@geopertea.bsky.social demonstrated setting up #Positron IDE 💻 by first detecting local interpreters and updating extensions 🔧. He showed how to login to @github.com to activate GitHub Copilot connectivity 🤖 for the Positron assistant. During the new installation, the app provides an... #RStats

I explained why including context is crucial 📚! I pointed out that someone could just paste code like "GRanges from 1 to 1000 plus..." but then I would be confused 😕 asking "where does this function come from? What package is this from?" 📦❓ @jennybryan.bsky.social #RStats #reprex

I demonstrated running a #reprex in a fresh #RStats session 💻 & opened it in my browser 🌐. It showed the 📦 loading with all its messages, then the function itself. I pointed out that I had made a syntax error: I missed the colon before the plus sign ➕❌, which caused an error @jennybryan.bsky.social

I explained how the reprex workflow helps with collaboration 🤝! I described a scenario where I ask a question about why the mean is 2.5 and not 3, and Nina wants to help by running the same code 💻. She can easily copy-paste the #reprex output and it actually runs ✅! @jennybryan.bsky.social #RStats

I demonstrated how to use the #reprex package 📦! I loaded it and explained the workflow: I copied lines of code from my console (pretending Leo has a question ❓), then ran the reprex() function without any arguments 💻. @jennybryan.bsky.social #RStats

I explained how a common problem makes it harder for people to get help 😤. People often think they've provided everything needed - posting their code online 💻, showing how to recreate objects, sharing all the code they ran, and even including the output 📊. @jennybryan.bsky.social #RStats #reprex