iiinova — where your digital self keeps evolving

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 22/09/2026

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

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Renee García-Flores @freneegf.bsky.social · 14/09/2026

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

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Renee García-Flores @freneegf.bsky.social · 16/09/2026

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

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Renee García-Flores @freneegf.bsky.social · 16/09/2026

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 😅)

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Christine Zhang @christinezhang.bsky.social · 13/09/2026

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/

Keynote Session by Christine Zhang, Graphics Editor at The New York Times: How to Be Clear When You Can’t Be Certain
Sometimes, data visualization is about using charts to illustrate a key point or conclusion gleaned from analyzing the data. But what if you’re not sure what the conclusion is? Presenting examples from news reporting on the topics of elections, polling and economics, I will talk about how I have grappled with uncertainty and how to communicate it to the public.

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Rob Patro @robp.bsky.social · 08/05/2026

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.

link.springer.com

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...

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 07/05/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 07/05/2026

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...

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 07/05/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 06/05/2026

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.

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Jenn Kim @drjennkim.bsky.social · 26/03/2026

@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/

research.libd.org

LIBD rstats club

Continuous rstats learning

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Jenn Kim @drjennkim.bsky.social · 26/03/2026

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-...

youtube.com

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

YouTube video by Leonardo Collado Torres

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 20/02/2026

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

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Crystal Lewis @cghlewis.bsky.social · 03/02/2026

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...

rdmweekly.substack.com

RDM Weekly - Issue 031

A weekly roundup of Research Data Management resources.

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 03/02/2026

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

@lieberinstitute.bsky.social @jhubiostat.bsky.social

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Nick Eagles @nick-eagles.bsky.social · 08/01/2026

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)!

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Nick Eagles @nick-eagles.bsky.social · 27/01/2026

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

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LIBD rstats club @libdrstats.bsky.social · 28/01/2026

@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

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LIBD rstats club @libdrstats.bsky.social · 28/01/2026

@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

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LIBD rstats club @libdrstats.bsky.social · 27/01/2026

@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

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LIBD rstats club @libdrstats.bsky.social · 27/01/2026

@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

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LIBD rstats club @libdrstats.bsky.social · 27/01/2026

@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

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LIBD rstats club @libdrstats.bsky.social · 27/01/2026

@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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

I explained the common problem people encounter when asking for coding help 🤔. I showed how someone might copy code they ran, paste it, ask a question. I was setting up to explain what's wrong with this approach ❌ of sharing code for troubleshooting purposes💻 #RStats #reprex @jennybryan.bsky.social

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 27/01/2026

I re-edited this 2020 video using Adobe Premier Pro's features for removing filler words, pauses, and text-based editing. In total it went down from 20:53 min to 12:41. I hope that you get to (re-)enjoy it ^_^. @jennybryan.bsky.social #RStats #reprex #reproducibility #JHPCE youtu.be/LfUFxHFhXTE

youtu.be

[2020-04-03] How to ask for R help by creating a small reproducible example (edited on 2026-01-27)

YouTube video by Leonardo Collado Torres

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Nick Eagles @nick-eagles.bsky.social · 16/01/2026

Lots has evolved since these R Stats sessions @libdrstats.bsky.social, but we touch on the hot topic of integrating LLMs into data science, mostly with Github Copilot, in a couple sessions-- Introductory look: youtu.be/xuCQZ5_5KB0 Reusable prompts: youtu.be/mlMl81xRI_M #RStats #LLMs

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Keri Martinowich @martinowk.bsky.social · 09/01/2026

Honored to be appointed Chief Scientific Officer @lieberinstitute.bsky.social. LIBD is a uniquely collaborative place with extraordinary biological resources and a commitment to translation 🧠🔬🧪. Grateful to my colleagues and excited to help guide our next chapter! www.libd.org/keri-martino...

libd.org

Keri Martinowich, Ph.D., Chief Scientific Officer | The Lieber Institute for Brain Development | Research & Discovery

Lieber Institute for Brain Development Appoints Keri Martinowich, Ph.D., as Chief Scientific Officer Baltimore, MD (January 6, 2025) — The Lieber Institute for Brain Development (LIBD) announced the a...

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 17/12/2025

PS You can see Cynthia's growth on @github.com by comparing the number of commits per year in 2022 (before joining @lieberinstitute.bsky.social), then the end of 2023, to 2025 (she spent nearly all year with us) 📈

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 17/12/2025

This is evident by topics she presented: * 13 times at @libdrstats.bsky.social (12 videos on YouTube) * 13 times at my team meeting (6 of them on YouTube) See also her 14 slide decks at speakerdeck.com/cyntsc/ www.youtube.com/@lcolladotor

speakerdeck.com

Cynthia SC (@cyntsc) on Speaker Deck

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Manisha Barse @mbarse.bsky.social · 05/12/2025

Hi! Check out my #RStats session on #R ’s object systems at @libdrstats.bsky.social - classes, objects, methods, & how all this drives our #bioinformatics workflows. Niche? Yes. But fascinating!⚙️🔧🧠✨ 🎥 youtu.be/EEqIJaDIb1I 🛝 speakerdeck.com/manishabarse... @lieberinstitute.bsky.social #OOP #S3 #S4

youtu.be

[2025-10-10] OOP in R: Understanding S3 and S4 systems

YouTube video by Leonardo Collado Torres

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Tim Triche, Jr.🔰 @timtriche.bsky.social · 01/12/2025

Yeah but also you have a tremendous group of people demonstrating that potential in the first place! It’s not enough to write papers, you must seize people’s attention so that they read the damned things 😁 Great work and just rewards.

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Nick Eagles @nick-eagles.bsky.social · 13/11/2025

Hot take: ggplot2 is better than any plotting option available in Python-- but I discuss a couple options in Python at an R Stats Club session @libdrstats.bsky.social linked below. I personally use plotnine, since it's essentially a port of ggplot2 for Python. youtu.be/xK9UNcOfjnI

youtu.be

[2025-07-18] Plots in Python with seaborn and plotnine

YouTube video by Leonardo Collado Torres

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 05/11/2025

Acá va en español 🇲🇽 --- o --- "¡Estamos orgullosos de anunciar que nuestro artículo ‘Análisis Transcriptómico de la Habénula Humana en Esquizofrenia’ es el artículo de portada de la edición de noviembre del American Journal of Psychiatry!" 🧠 #HabenulaLIBD #snRNAseq #Habénula doi.org/10.1176/appi...

doi.org

Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry

Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...

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Nick Eagles @nick-eagles.bsky.social · 04/11/2025

We recently checked out tidySingleCellExperiment at the R Stats Club @libdrstats.bsky.social, an R package part of a broader effort to bring tidy coding to genomics. Pretty useful! youtu.be/ob_SQY4-YjQ?... #RStats

youtu.be

[2025-07-11] Tidy manipulation of SingleCellExperiment objects

YouTube video by Leonardo Collado Torres

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Nick Eagles @nick-eagles.bsky.social · 13/06/2025

Just covered the data.table and dtplyr packages at LIBD R Stats Club @libdrstats.bsky.social. Really useful to be able to write dplyr code and get data.table performance! #rstats youtu.be/D3u64PMlJSI

youtu.be

[2025-06-13] Intro to data.table and dtplyr for data manipulation

YouTube video by Leonardo Collado Torres

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Heena Divecha @heenadivecha.bsky.social · 09/06/2025

App: r-graph-gallery.com/color-palett... Special thanks to @emilhvitfeldt.bsky.social for the {paletteer} package and to the @libdrstats.bsky.social club for fostering these practical #bioinformatics tips!

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Heena Divecha @heenadivecha.bsky.social · 09/06/2025

🎨 Struggling to pick the perfect color palette for data visualizations? Check out walkthrough of interactive tools and the awesome {paletteer} package by @emilhvitfeldt.bsky.social ! 🔗 youtu.be/9tAeTjVD7ns Let’s make our plots both beautiful and accessible! #RStats @libdrstats.bsky.social

youtu.be

Choosing a Color Palette

YouTube video by Leonardo Collado Torres

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Manisha Barse @mbarse.bsky.social · 06/06/2025

Hi everyone! Check my beginner-friendly #RStats talk at @lieberinstitute.bsky.social on reshaping, joining, binding, & set ops- all #tidyverse way! Shared simple demo to handle data better! 🎥 youtu.be/5L133h_1SNo 🛝 speakerdeck.com/manishabarse... @libdrstats.bsky.social #DataWrangling #DataScience

youtu.be

[2025-05-30] Reshaping data, Joining tables

YouTube video by Leonardo Collado Torres

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Nick Eagles @nick-eagles.bsky.social · 06/06/2025

Do a lot of PCA? Interested in streamlining data wrangling? In a couple recent LIBD R Stats Club @libdrstats.bsky.social sessions I talk about PCAtools, and dplyr for beginners. youtu.be/rClA0Ms-oOw youtu.be/XIbraIgPt0M #RStats

youtu.be

[2025-05-23] Introduction to dplyr for data manipulation

YouTube video by Leonardo Collado Torres

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Louise Huuki-Myers @lahuuki.bsky.social · 28/05/2025

Learning more about APOE differences in the cell types of the brain 🧠 I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease" from @zhaonaa.bsky.social at our team journal club, check it out! doi.org/10.1016/j.ne... ▶️ youtu.be/L4J9jFS-Pic

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