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🇲🇽 Leonardo Collado-Torres

@lcolladotor.bsky.social

3.9K followers 2.8K following 330 posts

#RStats @Bioconductor.bsky.social/🧠 genomics @lieberinstitute.bsky.social + Asst. Prof. @jhubiostat.bsky.social/@lcgunam @jtleek.bsky.social @aejaffe.bsky.social alumni/ @libdrstats.bsky.social @CDSBMexico.bsky.social http://lcolladotor.github.io

lcolladotor.github.io

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 12

Check our recent video "[2025-01-29] R/Bioconductor-powered Team Data Science: TLDR version 2025"
youtu.be/alL-g2roXxM

We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻

Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...

👥 go.bsky.app/53gy4UP

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Reposted by 🇲🇽 Leonardo Collado-Torres

Dr. Jean Fan @jef.works · 11d

In this blog post, I use #RStats to explore publicly available ICE arrest data. #Dataviz shows recent trend where ICE are primarily targeting/locating people without criminal records in communities.

Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial

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Reposted by 🇲🇽 Leonardo Collado-Torres

Keri Martinowich @martinowk.bsky.social · 13d

We have several positions open at various levels (Research Assistant, Research Associate, Postdoctoral Fellow) across our highly interactive teams in the Division of Translational Neuroscience 🧠🔬🧪 @lieberinstitute.bsky.social

www.libd.org/careers/

Links to individual positions in the thread below.

Careers at LIBD | Medical Research Jobs | Lieber Institute

View our career opportunities with Lieber Institute for Brain Development including investigators, medical research jobs, scientists, & lab techs

www.libd.org

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Reposted by 🇲🇽 Leonardo Collado-Torres

Kelly Bodwin @kellybodwin.com · 21d

I loved the "Hmmmmmm" in the crowd when @jcheng5.bsky.social showed this data quality problem uncovered by the #positron Databot tool.

No human caught this during the Tidy Tuesday for the data.

I've been skeptical of AI for data analysis, but this is an extremely compelling use case. 🫣

A slide showing that some rows of data have been systematically shifted left, leaving a missing data column and incorrect column alignment.

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Reposted by 🇲🇽 Leonardo Collado-Torres

Sharon Machlis @smachlis.bsky.social · Sep 3

Shiny app to search and filter posit::conf(2025) Bluesky posts with the #positconf2025 #positconf25 or #positconf hashtags.
App: apps.machlis.com/shiny/positc...
GitHub repo: github.com/smach/bluesk...
#RStats #RShiny

Screenshot of a web dashboard displaying Bluesky posts about posit::conf(2025), covering the period from January 8 to September 3, 2025.
Top summary boxes show:
* Total Posts: 61
* Unique Authors: 23
* Total Likes: 814
A searchable table lists individual posts with columns for CreatedAt, Text, Author, Likes, Reposts, Replies, and Tags. Four posts are visible including text, author, date, hashtags. (alt text mostly written by ChatGPT)

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Reposted by 🇲🇽 Leonardo Collado-Torres

Simon P. Couch @simonpcouch.com · 26d

@sara-altman.bsky.social and I just shared the second release of the Posit AI Newsletter! In this edition, a landmark settlement on LLM training data and copyright, the emergence of agentic browsers, and more.

Read and subscribe on the Posit Blog: posit.co/blog/2025-09...

A graphic displaying, on the left, three robot icons, and on the left, a selection of LLM-related R package hex stickers.

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Reposted by 🇲🇽 Leonardo Collado-Torres

Simon P. Couch @simonpcouch.com · Aug 29

So stoked to share about the first release of the Posit AI Newsletter!

@sara-altman.bsky.social and I have been working on a pilot of this newsletter internally for a few months now—an opinionated and pragmatic snapshot of AI news released every two weeks.

First edition: posit.co/blog/2025-08...

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Reposted by 🇲🇽 Leonardo Collado-Torres

Prashanthi Ravichandran @prashanthi-ravi.bsky.social · 23d

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

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Reposted by 🇲🇽 Leonardo Collado-Torres

Manisha Barse @mbarse.bsky.social · Sep 2

This paper reviews the latest computational approaches for cell-type deconvolution in spatial transcriptomics, comparing tools and data integration.

🔗 doi.org/10.1038/s415...

Thanks 🙌
@lgaspardboulinc.bsky.social, Luca Gortana, @thomas-walter.bsky.social, Emmanuel Barillot & Florence Cavalli

Cell-type deconvolution methods for spatial transcriptomics - Nature Reviews Genetics

Cell-type deconvolution methods are often needed to analyse spatial transcriptomic data to recover cell-type distributions. In this Review, the authors describe the process of cell-type deconvolution,...

doi.org

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Reposted by 🇲🇽 Leonardo Collado-Torres

Manisha Barse @mbarse.bsky.social · Sep 2

Hi everyone! Check my journal club talk on the latest review paper: Cell-type deconvolution methods for spatial transcriptomics 🧬

🎥 www.youtube.com/watch?v=xDjF...
🛝 speakerdeck.com/manishabarse

@lieberinstitute.bsky.social #Bioinformatics #SpatialTranscriptomics #Cell-TypeDeconvolution

[2025-08-13] Journal club: Cell-type deconvolution methods for spatial transcriptomics

YouTube video by Leonardo Collado Torres

www.youtube.com

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Aug 22

Ready to get the day started at @jhu.edu’s Schizophrenia Center Symposium day

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Reposted by 🇲🇽 Leonardo Collado-Torres

Lucy D’Agostino McGowan @lucystats.bsky.social · Aug 20

We are hiring into 3 (THREE!) tenure track lines this year at Wake Forest — if you’re looking please reach out, I love chatting about our department! We are a vibrant group that love & embrace the teacher-scholar model 👩‍🏫

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Reposted by 🇲🇽 Leonardo Collado-Torres

Dr. Jean Fan @jef.works · Jul 31

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

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...

hub.jhu.edu

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Reposted by 🇲🇽 Leonardo Collado-Torres

Dr. Jean Fan @jef.works · Jul 20

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

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Reposted by 🇲🇽 Leonardo Collado-Torres

NPR @npr.org · Jul 18

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)

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Reposted by 🇲🇽 Leonardo Collado-Torres

Dr. Jean Fan @jef.works · Jul 10

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

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 24

Indeed! Thanks for visiting us Hyejung! 🙌🏽

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Reposted by 🇲🇽 Leonardo Collado-Torres

Keri Martinowich @martinowk.bsky.social · Jun 24

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

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Reposted by 🇲🇽 Leonardo Collado-Torres

Hyejung Won @hyejungwon.bsky.social · Jan 27

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...

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.

www.cell.com

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Reposted by 🇲🇽 Leonardo Collado-Torres

Johns Hopkins Dept of Biostatistics @jhubiostat.bsky.social · Jun 20

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...

Dr. Leonardo Collado Torres | A Data Scientist Examines the Brain

YouTube video by Lieber Institute

www.youtube.com

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 12

* #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

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 12

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

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 12

* #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....

Better home for the DE analysis pipeline · Issue #11 · HelenaLC/muscat

In Section 14.3.3, there is a slightly complex edgeR-based analysis pipeline for cluster-wise pseudo-bulk DE analysis. I would prefer that the users not have to write this out every time they want ...

github.com

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 12

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

[2025-06-11] Pseudobulk DGE statistical methods journal club

YouTube video by Leonardo Collado Torres

youtu.be

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Reposted by 🇲🇽 Leonardo Collado-Torres

Hadley Wickham @hadley.nz · Jun 10

Happy 18th birthday ggplot2! #rstats

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.

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