Researchers at the @LieberInstitute learning, blogging & talking about #rstats, 📦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor
Baltimore, MD
Joined March 2018
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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.
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.…
@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)
👏🏽
@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 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
doi.org/10.64898/2025.12.18.…
LIBD rstats club retweeted
Boxiang @boxiangliu showcased #ISAAC for computing splicing QTLs #sQTLs using single cell data
They applied it to DLPFC 🧠 data from 722 donors
github.com/boxiangliulab/ISS…
#BoG2026 @cshlmeetings
LIBD rstats club retweeted
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 doi.org/10.1101/2025.07.02.6…
#BoG2026 @cshlmeetings
LIBD rstats club retweeted
Excited to announce that our #deconvolution benchmark has now been published in @GenomeBiology ! 📊
📄 doi.org/10.1186/s13059-025-0…
Check out my blog post for a high level overview: lahuuki.github.io/posts/2025…
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/10.1101/2024.02.09.5…
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
LIBD rstats club retweeted
Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq youtube.com/watch?v=mE77X5G-…; speakerdeck.com/cyntsc/clust… @LIBDrstats
LIBD rstats club retweeted
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/0…
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 retweeted
🆕 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!
LIBD rstats club retweeted
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
LIBD rstats club retweeted
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/s12864-024-1…
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/10.1101/2024.08.08.6…
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
👀 youtu.be/hclxkkp-V_I
LIBD rstats club retweeted
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 retweeted
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
LIBD rstats club retweeted
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!
LIBD rstats club retweeted
👋 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=xMsK…
![[2024-08-14] BICCN scATAC-seq paper journal club](https://pbs.twimg.com/card_img/2116819388716183552/cYJ69T4d?format=jpg&name=800x419)