LIBD rstats club
LightNews LightNews
banner
libdrstats.bsky.social
LIBD rstats club
@libdrstats.bsky.social
240 followers 92 following 28 posts
Researchers at the @lieberinstitute.bsky.social learning, blogging & talking about #rstats, 📦s, @Bioconductor.bsky.social, #bioinformatics (our own opinions) Admin: @lcolladotor.bsky.social

http://lieberinstitute.github.io/rstatsclub/
Posts Replies Media Videos
Pinned
libdrstats.bsky.social
LIBD rstats club @libdrstats.bsky.social · Nov 15
Here's our (small) starter pack of people who have presented at our club or whose recorded talks we have watched during our club meetings

Check docs.google.com/spreadsheets... for the full history of sessions + research.libd.org/rstatsclub/#... for our blog posts

#RStats

go.bsky.app/6z3UKe5
Reposted by LIBD rstats club
cghlewis.bsky.social
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
February 3, 2026 at 2:05 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
February 3, 2026 at 5:21 AM
Reposted by LIBD rstats club
nick-eagles.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)!
doi.org
January 8, 2026 at 6:00 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
January 27, 2026 at 7:53 PM
libdrstats.bsky.social
@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
January 28, 2026 at 2:59 AM
libdrstats.bsky.social
@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
January 28, 2026 at 2:50 AM
libdrstats.bsky.social
@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
January 27, 2026 at 9:22 PM
libdrstats.bsky.social
@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
January 27, 2026 at 9:12 PM
libdrstats.bsky.social
@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
January 27, 2026 at 9:04 PM
libdrstats.bsky.social
@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
January 27, 2026 at 8:54 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
January 27, 2026 at 8:16 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
January 27, 2026 at 8:06 PM
Reposted by LIBD rstats club
lcolladotor.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
January 27, 2026 at 7:58 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
January 27, 2026 at 7:49 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
January 27, 2026 at 7:44 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
January 27, 2026 at 7:41 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
[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
youtu.be
January 27, 2026 at 5:00 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
January 16, 2026 at 6:22 PM
Reposted by LIBD rstats club
martinowk.bsky.social
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...
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...
www.libd.org
January 9, 2026 at 1:07 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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) 📈
December 17, 2025 at 11:32 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
Cynthia SC (@cyntsc) on Speaker Deck
speakerdeck.com
December 17, 2025 at 11:24 PM
Reposted by LIBD rstats club
mbarse.bsky.social
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
[2025-10-10] OOP in R: Understanding S3 and S4 systems
YouTube video by Leonardo Collado Torres
youtu.be
December 5, 2025 at 5:27 PM
Reposted by LIBD rstats club
timtriche.bsky.social
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.
December 1, 2025 at 1:02 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
[2025-07-18] Plots in Python with seaborn and plotnine
YouTube video by Leonardo Collado Torres
youtu.be
November 13, 2025 at 3:02 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
Nuestros datos de #Habénula y de expresión diferencial pueden ser explorados vía sitios web interactivos 💻 #DatosLibres #iSEE 👀

github.com/LieberInstit...
GitHub - LieberInstitute/Habenula_Pilot: habenulaPilot project code repository
habenulaPilot project code repository. Contribute to LieberInstitute/Habenula_Pilot development by creating an account on GitHub.
github.com
November 5, 2025 at 11:47 PM