Researchers at the @LieberInstitute learning, blogging & talking about #rstats, π¦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor
Baltimore, MD
Joined March 2018
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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 ;)
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.
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
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
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
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¦
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
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
LIBD rstats club retweeted
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¦
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¦
LIBD rstats club retweeted
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!
LIBD rstats club retweeted
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
![[2025-01-31] R coding using GitHub Copilot with RStudio and related R packages](https://pbs.twimg.com/card_img/2115355372718346240/4Z3lIr7D?format=jpg&name=800x419)
LIBD rstats club retweeted
Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq youtube.com/watch?v=mE77X5G-β¦; speakerdeck.com/cyntsc/clustβ¦ @LIBDrstats
LIBD rstats club retweeted
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
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
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
teapawt.net/teichlab/status/180518β¦
LIBD rstats club retweeted
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!
LIBD rstats club retweeted
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
LIBD rstats club retweeted
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¦
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¦
LIBD rstats club retweeted
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
LIBD rstats club retweeted
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
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
