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Find us as @LIBDrstats.🌌.social ;)
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LIBD rstats club
867 posts
LIBD rstats club
@LIBDrstats
Researchers at the @LieberInstitute learning, blogging & talking about #rstats, 📦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor
Baltimore, MD Katılım Mart 2018
204 Takip Edilen407 Takipçiler
LIBD rstats club retweetledi
Excited to announce that our #deconvolution benchmark has now been published in @GenomeBiology ! 📊
📄 doi.org/10.1186/s13059…
Check out my blog post for a high level overview: lahuuki.github.io/posts/2025-04-…
Louise Huuki-Myers@lahuuki
Hey #deconvolution fans! 👀 We’ve got an exciting new pre-print for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬 @LieberInstitute @jhubiostat #scitwitter 📎 doi.org/10.1101/2024.0…
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LIBD rstats club retweetledi
A few months late, but here's our @libdrstats "End of year GitHub cleanup" 2024 activity guidelines
youtu.be/MrMae8vikGQ
< 5 min
Thank you all #OpenSource developers who make #RStats and other software we depend on!
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LIBD rstats club retweetledi
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
youtu.be/qWuoVQG5BZw
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LIBD rstats club retweetledi
Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq youtube.com/watch?v=mE77X5…; speakerdeck.com/cyntsc/cluster… @LIBDrstats
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LIBD rstats club retweetledi
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/03/14/ini…
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
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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
📼 youtu.be/0D6l01ArI9M
YouTube
🇲🇽 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 📜 doi.org/10.1093/bioinf… 🛝 speakerdeck.com/nickeagles/exp… 📽️ youtu.be/ZY9N4spEZ_Q @10xGenomics twitter.com/teichlab/statu…
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LIBD rstats club retweetledi
🆕 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!
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LIBD rstats club retweetledi
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
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LIBD rstats club retweetledi
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
doi.org/10.1186/s12864…
🇲🇽 Leonardo Collado-Torres@lcolladotor
Is your tissue larger than a @10xGenomics Visium capture area? If you need to stitch together the images but also the gene expression data, check our new preprint describing #visiumStitched We also shared example postmortem human brain data (3 samples) doi.org/10.1101/2024.0…
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LIBD rstats club retweetledi
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
👀 youtu.be/hclxkkp-V_I
YouTube
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LIBD rstats club retweetledi
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
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For more info on Manisha check manishabarse.github.io
@LieberInstitute
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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
🛝 speakerdeck.com/manishabarse/e…
📽️ youtu.be/cJqsbDh0ZtI
Data viz with #RStats
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LIBD rstats club retweetledi
Today at @LIBDrstats we did some live debugging on 2 @Bioconductor 📦s we submitted
* #visiumStitched: we tried reproducing a Single Package Builder error
* #DeconvoBuddies: we discussed options to comply with the 15 min limit to "R CMD build"
#RStats
youtu.be/YAeUsKGUmtM
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LIBD rstats club retweetledi
When you choose to donate to us, you can do it with the full confidence that your money is carefully and thoughtfully used. We’ve earned our Platinum Seal of Transparency with @CandidDotOrg!
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LIBD rstats club retweetledi
👋 Looking for something insightful to dive into this weekend? Check out my talk where I summarize the paper 'A Comparative Atlas of Single-Cell Chromatin Accessibility in the Human Brain.' It's packed with valuable insights—hope you find it informative! youtu.be/1b_AsFYlEB0?si…
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LIBD rstats club retweetledi
I presented at @LIBDrstats an overview on Multicellular Factor Analysis #MFA & Multi-Omics Factor Analysis #MOFA 🧫
Includes shoutouts to @OliverStegle @wolfgangkhuber @saezlab @roramirezf94
🗒️ docs.google.com/document/d/1fk…
📽️ youtu.be/PN6q_uaVCjI
#MOFAcellulaR #LIANA+ #RStats
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LIBD rstats club retweetledi
Thanks Kate Smith & the Faculty Orientation team for organizing the 1st welcome event for new @JohnsHopkinsSPH faculty hosted by @EllenJMacKenzie
It was an honor to represent @jhubiostat 🙌🏽, though clearly we were outnumbered by @JohnsHopkinsIH! I met 8+ new IH faculty tonight!
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LIBD rstats club retweetledi
Having received a @Conahcyt_Mex PhD scholarship, Leo gives back by teaching at @lcgunam @lcgejunam ~1 week/year and co-founded @CDSBMexico to Latin Americans like him break through and start their careers in computational biology, particularly using #RStats & @Bioconductor
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