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...

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

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

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

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

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...

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) 📈

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

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

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.

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

Nuestros datos de #Habénula y de expresión diferencial pueden ser explorados vía sitios web interactivos 💻 #DatosLibres #iSEE 👀 github.com/LieberInstit...

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...

#OpenData and #OpenCode from our latest @lieberinstitute.bsky.social project Lots of #RStats and @bioconductor.bsky.social code inside of that repository! #OpenScience

Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...

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

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

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!

🎨 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

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

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

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

I've used in our recent @libdrstats.bsky.social and team videos. That's why many are significantly shorter now: * 12 min saved on an hour long video * a 20:45 min video to 13:13 * a 40:59 to 27:40 * a 31:49 to 23:52 * a 20:30 to 17:44 Videos are fluid too. I recommend trying out these features!

Last month at @libdrstats.bsky.social LIBD #rstats club I showed a #GenAI multi-modal LLM prompting technique for planning and scaffolding a R-Shiny + bslib application, using Google AI Studio, with VisualStudio Code as the IDE for R development (only free tools). youtu.be/7PA45mVxZ8M

Presented at @lieberinstitute.bsky.social #RStats club on pseudobulk analysis using pseudoBulkDGE()📊 A handy wrapper for DE analysis following OSCA guidelines-shared a demo & walked through the method!✨ 🎥 youtu.be/0OkWBLyLrfg 🛝 speakerdeck.com/manishabarse... @libdrstats.bsky.social #Bioinformatics

Check out my LIBD @lieberinstitute.bsky.social R Stats Club #rstats presentation on SLURM array jobs for efficient parallel data analysis on HPC systems-- #slurm #hpc youtu.be/Sz7LpAC1gsQ

Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression🧬 Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach🙌 🎥 youtu.be/zpeCFwYfV3o 🛝 speakerdeck.com/manishabarse #snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social

This paper was an exciting culmination of a lots of exploration with #deconvolution ! Check-out my blog post on this work for the TL;DR version: lahuuki.github.io/posts/2025-0...

We also propose and evaluate a new method for selecting cell type specific #markergenes for deconvolution: #MeanRatio implemented in #DeconvoBuddies @bioconductor.bsky.social #rstats 🛠️ research.libd.org/DeconvoBuddi...

Hey #deconvolution fans! 👀 We’ve got an exciting new publication for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬 Now out in Genome Biology: doi.org/10.1186/s130... @lieberinstitute.bsky.social @jhubiostat.bsky.social

New blog post: Initial impressions from testing Posit Connect lcolladotor.github.io/2025/03/14/i... I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward @posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE

🚀 Interested in multimodal analysis with WNN in Seurat? Check out my recent RStatClub presentation, where we dive into Jaccard, canonical gene expression, and Silhouette for clustering evaluation! 📺 Watch here: speakerdeck.com/cyntsc/clust... 📑 Slides: www.youtube.com/watch?v=mE77... #RStats

I’m disappointed by @cziscience.bsky.social’s decision to discontinue the Science Diversity Leadership Award chanzuckerberg.com/rfa/science-... no longer exists. But we exist & science needs us❤️‍🔥 👀 previous info at web.archive.org/web/20250130... I’m among those who had written a Letter of Intent

After teaching #LCG-UNAM students about these tools, at @libdrstats.bsky.social I talked about "R coding using GitHub Copilot with RStudio and related R packages" Shoutouts @simonpcouch.com @theotheredgar.bsky.social @hadley.nz et al! #RStats @posit.co youtu.be/qWuoVQG5BZw

Check out my journal club presentation on the crumblr pre-print from Hoffman and Roussos, a new method to analyze differential composition in #singlecell data 🍪 Looks very useful for single cell RNA-seq data with case/control study design 🤔 📄 doi.org/10.1101/2025... ▶️ www.youtube.com/watch?v=Hi5E...

A few months late, but here's our @libdrstats.bsky.social "End of year GitHub cleanup" 2024 activity guidelines youtu.be/MrMae8vikGQ < 5 min video Thank you all #OpenSource developers who make #RStats and other software we depend on!