🇲🇽 Leonardo Collado-Torres

University labs help power America's biotech innovation ecosystem Hopkins researcher Jean Fan and her team create open-source tools that help bridge the gap between academic discoveries and life-saving treatments. Cuts to federal funding threaten to break this criti...

In this interview, I explain how university research, when funded by independent #NIH #NSF federal grants, brings oversight to biotech to fuel innovation while keeping science transparent, reliable, and in service of the public good: hub.jhu.edu/2025/07/30/j...

#ResearchMatters

I visualize trends in #ICE #immigration arrests and encounters over time and across select US cities using public data from deportationdata.org/data/ice.html

Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7...

#codetutorial

Congress has decided to claw back previously approved funding for public media.

This decision hurts people in communities across the country, but it has only strengthened our resolve to keep Americans informed and connected. (1/2)

The point of LLMs is to make rich guys feel like they are also smart guys

In this blog post, I use #RStats to analyze ICE detention data. #Datavisualization shows record numbers of detainees without any criminal records. Further more/bigger ICE facilities are popping up far from the border.

Code along and take a look for yourself: jef.works/blog/2025/07...

#CodeTutorial

Indeed! Thanks for visiting us Hyejung! 🙌🏽

Phenomenal talk from @hyejungwon.bsky.social who is visiting us @lieberinstitute.bsky.social for the day. Groundbreaking work w/ important implications and roadmap for using rapidly emerging information on psychiatric genetics to prioritize variants and understand their impact on 🧠 function

Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders High-throughput experimental validation of genetic variants linked to eight psychiatric disorders reveals the regulatory mechanisms underlying variants with pleiotropic and disorder-specific effects.

1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders.
www.cell.com/cell/abstrac...

YouTube video by Lieber Institute Dr. Leonardo Collado Torres | A Data Scientist Examines the Brain

Biostats assistant professor @lcolladotor.bsky.social is also an investigator @lieberinstitute.bsky.social where he leads the R/Bioconductor-powered Team Data Science group. Learn more about his work in the video below: www.youtube.com/watch?v=Rz4L...

* #dreamlet: linear mixed model that can handle random effects (good for ""batch""), uses voom, computationally efficient, nice @bioconductor.bsky.social package EDA tools

* #distinct: based on comparing empirical cumulative distribution (ECDs) curves

* Differential Detection: you can find biologically-relevant genes missed by DE methods, based on pseudo-bulking 0s and 1s. Implemented as #muscat::pbDD().

* #muscat: pseudo-bulk methods perform best, that #edgeR beats #voom for small sample sizes. #scran::pseudobulkDGE() was inspired by #muscat::pbDS() as noted at github.com/HelenaLC/mus....

YouTube video by Leonardo Collado Torres [2025-06-11] Pseudobulk DGE statistical methods journal club

Pseudobulk DGE #RStats journal club

* #muscat doi.org/10.1038/s414... @helucro.bsky.social
* pbDD doi.org/10.1101/2023... @davi1893.bsky.social
* #dreamlet doi.org/10.1101/2023... ‪@panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social

youtu.be/TB9dfKPfns8

Balloon wall art inspired by the ggplot2 hex sticker. The display features a hexagonal frame made of black balloons, filled with white balloons inside and surrounded by a background of light and dark blue balloons. A line graph with black balloon segments and round coloured nodes runs across the centre, and the word “ggplot2” is spelled out in black balloon letters below the chart.

Happy 18th birthday ggplot2! #rstats

#SpotSweeper is now published!

Check our journal club session summary of the pre-print version by @lahuuki.bsky.social

The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!

youtu.be/f72XcXmtkfw?...

Welcome @heenadivecha.bsky.social to Bsky! ^_^

Heena is a great scientist who worked at @lieberinstitute.bsky.social before joining @jhu.edu as a PhD student, and who is now back doing her PhD with @kr-maynard.bsky.social at LIBD

🔁

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!

YouTube video by Leonardo Collado Torres Choosing a Color Palette

🎨 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

YouTube video by Leonardo Collado Torres [2025-05-30] Reshaping data, Joining tables

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

SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...

🚨 New paper published in @natmethods.nature.com!

We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.

📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/

🧵👇

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats!

Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

YouTube video by Leonardo Collado Torres [2025-05-23] Introduction to dplyr for data manipulation

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

[…] great budding projects 🌱 but also to serve the student. To help them in their journey.

Time flew by!

I’m looking forward to witnessing the student’s growth. But also I’m going to try to learn from the experience and apply it to my work at @lieberinstitute.bsky.social

New career milestone: served on a @jhu.edu PhD thesis committee meeting for the first time 🙌🏽

Thanks @jef.works for inviting me! And thanks @mikeschatz.bsky.social @jihk.bsky.social for your guidance! Great to share this experience with Fred Tan as well ^_^

It’s exciting to talk about […]

ellmer 0.2.0 ellmer 0.2.0 lands with a swag of upgrades: Garrick Aden‑Buie joins the team, we make a couple of breaking changes, and add serious scale with `parallel_chat()` and `batch_chat()`. A new `params()` ...

Want to easily use LLMs from R? ellmer 0.2.0 provides:

• Batch & parallel processing
• A universal parameter interface
• Cost tracking
• Support for Mistral, Hugging Face, & Portkey

And much more! Read all about it at: www.tidyverse.org/blog/2025/05... #rstats

YouTube video by Leonardo Collado Torres [2025-05-21] Journal club on brain multiome papers

🔬 Diving into ATAC-seq workflows?
You've likely heard about Seurat, Signac, MACS2, Cicero, and chromVAR—core components in many workflows.
Here’s a quick overview I put together that showcases different approaches used across recent studies.
youtu.be/R5P8mGMXuIg?...
#SingleCell #Epigenomics #LIBD

Used it in*

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

Kinnary Shah is a fourth-year PhD candidate and co-president of the Biostats Student Org. Learn more about Kinnary and two of her ongoing research projects, one with the @lieberinstitute.bsky.social, and one with @stephaniehicks.bsky.social, on our website:
publichealth.jhu.edu/departments/...

YouTube video by Leonardo Collado Torres [2025-04-11] Scaffolding R-Shiny apps with generative AI

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