LIBD rstats club

Researchers at the @LieberInstitute learning, blogging & talking about #rstats, 📦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor

[LIBD rstats club @LIBDrstats]

We just created our new profile on that social media network people have been joining recently! See you there!

Find us as @LIBDrstats.🌌.social ;)

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Yoav @Y_Gilad kickstarts #BoG2026 at @cshlmeetings by asking us to be open minded and think beyond biology defined by means. To think about the dispersion / variance.

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Aoxing @aoxing2 gave a great talk at #BoG2026 (even more considering it was last minute promoted to a talk!) on studying sex chromosome dosage thanks to available biobank data from rare but tolerated sex chromosome trisomies

Builds upon https://t.co/xL9UABCPfC

@cshlmeetings

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Mike @mike_schatz paid tribute to James P. Taylor @jxtx who was one of the main champions of #OpenScience

To carry on Mike et al founded @jxtxFoundation & introduced the winners of the scholarship to attend #BoG2026 this year (sponsored by @PacBio this year)

👏🏽

@cshlmeetings

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Did you miss #BoG2026 or want to share your work or want to keep learning about great computational biology? Mike @mike_schatz invites us to #BDS26 later this year in November

Check https://t.co/ojI4bDNnuj for all the details!

@cshlmeetings

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

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

https://t.co/1yFnxfMjta

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Boxiang @boxiangliu showcased #ISAAC for computing splicing QTLs #sQTLs using single cell data

They applied it to DLPFC 🧠 data from 722 donors

https://t.co/blZ5F3qbcY

#BoG2026 @cshlmeetings

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Megan D. Schertzer from @davidaknowles.’s lab invites us to use « perplexity » from Ecology to measure isoform diversity (or other molecular units).

Very thought provoking! 🤔

More at https://t.co/0LFzrhVljG

#BoG2026 @cshlmeetings

[Louise Huuki-Myers @lahuuki]

Excited to announce that our #deconvolution benchmark has now been published in @GenomeBiology ! 📊
📄 https://t.co/A3oQERcuqF
Check out my blog post for a high level overview: https://t.co/WtyplwOi0e

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

A few months late, but here's our @libdrstats "End of year GitHub cleanup" 2024 activity guidelines

https://t.co/DSTIn8tStY

< 5 min

Thank you all #OpenSource developers who make #RStats and other software we depend on!

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

After teaching @lcgunam students about these tools, at @libdrstats I talked about "R coding using GitHub Copilot with RStudio and related R packages"

Shoutouts @simonpcouch @theotheredgar @hadleywickham et al! #RStats @posit_pbc

https://t.co/A3kZMKGckl

[Cynthia SC @cynthiasotocar]

Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq https://t.co/V6irPi2ydQ; https://t.co/ZrQKXCjrgJ @LIBDrstats

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

New blog post: Initial impressions from testing Posit Connect
https://t.co/lq0eJ3OiQF

I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute work moving forward

@posit_pbc #RStats #shiny #shinyapps #spatialLIBD #iSEE @LIBDrstats

[LIBD rstats club @LIBDrstats]

Check out this journal club presentation by Nick Eagles on:

> #ENACT: End-to-End Analysis of Visium High Definition (HD) Data

Nick also compared #ENACT against #bin2cell

#VisiumHD @10xgenomics #PyStats

📼 https://t.co/dGfj10pY2g

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

🆕 journal club by Nick Eagles

"#Bin2cell reconstructs cells from high resolution #VisiumHD data" by Polański @RBartolom et al from @teichlab @YayonNadav labs

📜 https://t.co/AywC9MYEjm
🛝 https://t.co/eVcVdwrkID
📽️ https://t.co/nQ63fEW3tG

@10xGenomics

https://t.co/ih32nJpGGV

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

🆕 improved diagram for how #visiumStitched is able to help #BayesSpace, #PRECAST, & other array-based methods (col/row hex grid) find more neighboring spots when you have overlapping spots from different capture areas.

You already generated the 🤩 data, might as well use it!

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

One 💯 update is how Nick used the overlapping spots to calculate a matching rate in spatial cluster assignments

#BayesSpace with HVGs does better, whereas #PRECAST with #nnSVG SVGs does slightly better. Both improve when using #visiumStitched to increase the number of neighbors

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

I'm thrilled to share with you that #visiumStitched led by Nick Eagles has now been published

Our #RStats / @Bioconductor 📦provides a framework for stitching together multiple #Visium @10xgenomics capture areas together

https://t.co/T5SIJjrKY2

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

Today for @LIBDrstats I led a "Live exploration of latest #RStats news on Bluesky"

Bluesky intro: starter packs & feeds (aka algorithms)

+ @hadleywickham's curated feed, @Bioconductor news, and more

👀 https://t.co/6OCrX5GNhb

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

I made a genomic scientists trained in Mexico 🇲🇽
starter pack. I'd like for our voices to be heard!

If you can help spread the word, that'd be great!

Thank you!

@CDSBMexico @nnb_unam @RBioinformatica @lcgunam @lcgunam @ccg_unam @ibt_unam @LIIGH_UNAM

[LIBD rstats club @LIBDrstats]

Check the Zoom AI summary below:

[LIBD rstats club @LIBDrstats]

Manisha Barse presented with us for the first time!

She explained the metrics summary CSV files generated by SpaceRanger by @10xGenomics when processing #Visium spatially-resolved transcriptomics data

🛝 https://t.co/swgMAFKnIM
📽️ https://t.co/5F6YpBf7eW

Data viz with #RStats

[LIBD rstats club @LIBDrstats]

For more info on Manisha check https://t.co/8QJrx5QJkM

@LieberInstitute