LIBD rstats club
@LIBDrstats
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Researchers at the @LieberInstitute learning, blogging & talking about #rstats, π¦s, @Bioconductor, #bioinformatics (our own opinions) Admin: @lcolladotor
Baltimore, MD
Joined March 2018
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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Excited to announce that our #deconvolution benchmark has now been published in @GenomeBiology ! π π https://t.co/A3oQERcuqF Check out my blog post for a high level overview:
genomebiology.biomedcentral.com
Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the...
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 https://t.co/4KXibeerZi
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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!
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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
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Sharing from our RStatClub: Clustering methods in multiome scRNA-seq and scATAC-seq https://t.co/V6irPi2ydQ;
https://t.co/ZrQKXCjrgJ
@LIBDrstats
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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
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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 πΌ
π journal club by Nick Eagles "#Bin2cell reconstructs cells from high resolution #VisiumHD data" by PolaΕski @RBartolom et al from @teichlab @YayonNadav labs π https://t.co/AywC9MYEjm π https://t.co/eVcVdwrkID π½οΈ https://t.co/nQ63fEW3tG
@10xGenomics
https://t.co/ih32nJpGGV
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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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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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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 https://t.co/T5SIJjrKY2
bmcgenomics.biomedcentral.com
Background Visium is a widely-used spatially-resolved transcriptomics assay available from 10x Genomics. Standard Visium capture areas (6.5mm by 6.5mm) limit the survey of larger tissue structures,...
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) https://t.co/sYMH2V10JE
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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
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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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For more info on Manisha check https://t.co/8QJrx5QJkM
@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 π https://t.co/swgMAFKnIM π½οΈ https://t.co/5F6YpBf7eW Data viz with #RStats
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Today at @LIBDrstats we did some live debugging on 2 @Bioconductor π¦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
https://t.co/nZlNXSAalt
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When you choose to donate to us, you can do it with the full confidence that your money is carefully and thoughtfully used. Weβve earned our Platinum Seal of Transparency with @CandidDotOrg!
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π 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 insightsβhope you find it informative!
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I presented at @LIBDrstats an overview on Multicellular Factor Analysis #MFA & Multi-Omics Factor Analysis #MOFA 𧫠Includes shoutouts to @OliverStegle @wolfgangkhuber @saezlab @roramirezf94 ποΈ https://t.co/kxpCxRxuvj π½οΈ https://t.co/9p2t22muSN
#MOFAcellulaR #LIANA+ #RStats
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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 ππ½, though clearly we were outnumbered by @JohnsHopkinsIH! I met 8+ new IH faculty tonight!
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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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