Researchers at the @LieberInstitute learning, blogging & talking about #rstats, π¦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor
Joined March 2018
- Tweets 873
- Following 204
- Followers 402
- Likes 841
105 Photos and videos
Pinned Tweet
20 Sep 2023
We just created our new profile on that social media network people have been joining recently! See you there!
Find us as @LIBDrstats.π.social ;)
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LIBD rstats club retweeted
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.
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LIBD rstats club retweeted
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 doi.org/10.1016/j.ajhg.2025.β¦
@cshlmeetings
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LIBD rstats club retweeted
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)
ππ½
@cshlmeetings
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LIBD rstats club retweeted
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 bit.ly/cshl-biodata26 for all the details!
@cshlmeetings
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LIBD rstats club retweeted
Brian Clearlyβs work on Β« Fundamental errors in #RNAvelocity arising from the omission of cell growth Β» feels like a must read!!
Brian shouted out the co-authors in the second slide ππ½
#BoG2026 @cshlmeetings
doi.org/10.64898/2025.12.18.β¦
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LIBD rstats club retweeted
Boxiang @boxiangliu showcased #ISAAC for computing splicing QTLs #sQTLs using single cell data
They applied it to DLPFC π§ data from 722 donors
github.com/boxiangliulab/ISSβ¦
#BoG2026 @cshlmeetings
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LIBD rstats club retweeted
Megan D. Schertzer from @davidaknowles.βs lab invites us to use Β« perplexity Β» from Ecology to measure isoform diversity (or other molecular units).
Very thought provoking! π€
More at doi.org/10.1101/2025.07.02.6β¦
#BoG2026 @cshlmeetings
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LIBD rstats club retweeted
9 Apr 2025
Excited to announce that our #deconvolution benchmark has now been published in @GenomeBiology ! π
π doi.org/10.1186/s13059-025-0β¦
Check out my blog post for a high level overview: lahuuki.github.io/posts/2025β¦
15 Apr 2024
Hey #deconvolution fans! π Weβve got an exciting new pre-print for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset π§ 𧬠@LieberInstitute @jhubiostat #scitwitter
π doi.org/10.1101/2024.02.09.5β¦
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LIBD rstats club retweeted
13 Feb 2025
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 retweeted
13 Feb 2025
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 retweeted
13 Feb 2025
Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq youtube.com/watch?v=mE77X5G-β¦; speakerdeck.com/cyntsc/clustβ¦ @LIBDrstats
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LIBD rstats club retweeted
14 Mar 2025
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/0β¦
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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22 Nov 2024
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
πΌ youtu.be/0D6l01ArI9M
9 Oct 2024
π journal club by Nick Eagles
"#Bin2cell reconstructs cells from high resolution #VisiumHD data" by PolaΕski @RBartolom et al from @teichlab @YayonNadav labs
π doi.org/10.1093/bioinformatiβ¦
π speakerdeck.com/nickeagles/eβ¦
π½οΈ youtu.be/ZY9N4spEZ_Q
@10xGenomics
x.com/teichlab/status/180518β¦
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LIBD rstats club retweeted
18 Nov 2024
π 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 π€© data, might as well use it!
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LIBD rstats club retweeted
18 Nov 2024
One π― 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 retweeted
18 Nov 2024
I'm thrilled to share with you that #visiumStitched led by Nick Eagles has now been published
Our #RStats / @Bioconductor π¦provides a framework for stitching together multiple #Visium @10xgenomics capture areas together
doi.org/10.1186/s12864-024-1β¦
12 Aug 2024
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/10.1101/2024.08.08.6β¦
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LIBD rstats club retweeted
15 Nov 2024
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
π youtu.be/hclxkkp-V_I
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LIBD rstats club retweeted
8 Nov 2024
I made a genomic scientists trained in Mexico π²π½
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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7 Nov 2024
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
π speakerdeck.com/manishabarseβ¦
π½οΈ youtu.be/cJqsbDh0ZtI
Data viz with #RStats
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