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LIBD rstats club

@libdrstats.bsky.social

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Researchers at the @lieberinstitute.bsky.social learning, blogging & talking about #rstats, 📦s, @Bioconductor.bsky.social, #bioinformatics (our own opinions) Admin: @lcolladotor.bsky.social http://lieberinstitute.github.io/rstatsclub/

lieberinstitute.github.io

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LIBD rstats club @libdrstats.bsky.social · Nov 15

Here's our (small) starter pack of people who have presented at our club or whose recorded talks we have watched during our club meetings

Check docs.google.com/spreadsheets... for the full history of sessions + research.libd.org/rstatsclub/#... for our blog posts

#RStats

go.bsky.app/6z3UKe5

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Nick Eagles @nick-eagles.bsky.social · Jun 13

Just covered the data.table and dtplyr packages at LIBD R Stats Club @libdrstats.bsky.social. Really useful to be able to write dplyr code and get data.table performance!

#rstats

youtu.be/D3u64PMlJSI

[2025-06-13] Intro to data.table and dtplyr for data manipulation

YouTube video by Leonardo Collado Torres

youtu.be

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Heena Divecha @heenadivecha.bsky.social · Jun 9

App: r-graph-gallery.com/color-palett...

Special thanks to @emilhvitfeldt.bsky.social for the {paletteer} package and to the @libdrstats.bsky.social club for fostering these practical #bioinformatics tips!

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Heena Divecha @heenadivecha.bsky.social · Jun 9

🎨 Struggling to pick the perfect color palette for data visualizations? Check out walkthrough of interactive tools and the awesome {paletteer} package by @emilhvitfeldt.bsky.social !

🔗 youtu.be/9tAeTjVD7ns

Let’s make our plots both beautiful and accessible!
#RStats @libdrstats.bsky.social

Choosing a Color Palette

YouTube video by Leonardo Collado Torres

youtu.be

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Manisha Barse @mbarse.bsky.social · Jun 6

Hi everyone! Check my beginner-friendly #RStats talk at @lieberinstitute.bsky.social on reshaping, joining, binding, & set ops- all #tidyverse way! Shared simple demo to handle data better!

🎥 youtu.be/5L133h_1SNo
🛝 speakerdeck.com/manishabarse...

@libdrstats.bsky.social #DataWrangling #DataScience

[2025-05-30] Reshaping data, Joining tables

YouTube video by Leonardo Collado Torres

youtu.be

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Nick Eagles @nick-eagles.bsky.social · Jun 6

Do a lot of PCA? Interested in streamlining data wrangling? In a couple recent LIBD R Stats Club @libdrstats.bsky.social sessions I talk about PCAtools, and dplyr for beginners.

youtu.be/rClA0Ms-oOw
youtu.be/XIbraIgPt0M

#RStats

[2025-05-23] Introduction to dplyr for data manipulation

YouTube video by Leonardo Collado Torres

youtu.be

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Louise Huuki-Myers @lahuuki.bsky.social · May 28

Learning more about APOE differences in the cell types of the brain 🧠

I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease" from @zhaonaa.bsky.social at our team journal club, check it out!

doi.org/10.1016/j.ne...

▶️ youtu.be/L4J9jFS-Pic

Redirecting

doi.org

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · May 28

I've used in our recent @libdrstats.bsky.social and team videos. That's why many are significantly shorter now:

* 12 min saved on an hour long video
* a 20:45 min video to 13:13
* a 40:59 to 27:40
* a 31:49 to 23:52
* a 20:30 to 17:44

Videos are fluid too. I recommend trying out these features!

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Geo @geopertea.bsky.social · May 27

Last month at @libdrstats.bsky.social LIBD #rstats club I showed a #GenAI multi-modal LLM prompting technique for planning and scaffolding a R-Shiny + bslib application, using Google AI Studio, with VisualStudio Code as the IDE for R development (only free tools).
youtu.be/7PA45mVxZ8M

[2025-04-11] Scaffolding R-Shiny apps with generative AI

YouTube video by Leonardo Collado Torres

youtu.be

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Manisha Barse @mbarse.bsky.social · May 23

Presented at @lieberinstitute.bsky.social #RStats club on pseudobulk analysis using pseudoBulkDGE()📊 A handy wrapper for DE analysis following OSCA guidelines-shared a demo & walked through the method!✨
🎥 youtu.be/0OkWBLyLrfg
🛝 speakerdeck.com/manishabarse...

@libdrstats.bsky.social #Bioinformatics

[2025-05-02] pseudobulk analysis with pseudoBulkDGE()

YouTube video by Leonardo Collado Torres

www.youtube.com

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Nick Eagles @nick-eagles.bsky.social · May 23

Check out my LIBD @lieberinstitute.bsky.social R Stats Club #rstats presentation on SLURM array jobs for efficient parallel data analysis on HPC systems--

#slurm #hpc

youtu.be/Sz7LpAC1gsQ

[2025-04-04] Writing nested array jobs at JHPCE and designing run_all.sh scripts

YouTube video by Leonardo Collado Torres

youtu.be

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Reposted by LIBD rstats club

Manisha Barse @mbarse.bsky.social · May 22

Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression🧬

Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach🙌

🎥 youtu.be/zpeCFwYfV3o
🛝 speakerdeck.com/manishabarse

#snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social

[2025-04-23] Journal club on "[...] deconvolution of pooled snRNA-seq using sex-dependent gene expr"

YouTube video by Leonardo Collado Torres

youtu.be

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Louise Huuki-Myers @lahuuki.bsky.social · Apr 11

This paper was an exciting culmination of a lots of exploration with #deconvolution ! Check-out my blog post on this work for the TL;DR version: lahuuki.github.io/posts/2025-0...

Deconvolution Benchmark: TL;DR – Louise A. Huuki-Myers

A high level overview of the Deconvolution Benchmark project, now published in Genome Biology!

lahuuki.github.io

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Louise Huuki-Myers @lahuuki.bsky.social · Apr 11

We also propose and evaluate a new method for selecting cell type specific #markergenes for deconvolution: #MeanRatio implemented in #DeconvoBuddies
@bioconductor.bsky.social #rstats
🛠️ research.libd.org/DeconvoBuddi...

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Louise Huuki-Myers @lahuuki.bsky.social · Apr 11

Hey #deconvolution fans! 👀 We’ve got an exciting new publication for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬
Now out in Genome Biology: doi.org/10.1186/s130...

@lieberinstitute.bsky.social @jhubiostat.bsky.social

Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex - Genome Biology

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 h...

doi.org

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Mar 14

New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/03/14/i...

I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward

@posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE

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Cynthia SC @cynthiasc.bsky.social · Feb 13

🚀 Interested in multimodal analysis with WNN in Seurat?
Check out my recent RStatClub presentation, where we dive into Jaccard, canonical gene expression, and Silhouette for clustering evaluation!
📺 Watch here: speakerdeck.com/cyntsc/clust...
📑 Slides: www.youtube.com/watch?v=mE77...
#RStats

Clustering methods in multiome scRNA-seq and scATAC-seq

Main topics covered on this talk: Introducing the Weighted-Nearest Neighbor (WNN) for multimodal analysis A glance of WNN clustering algorithms availa…

speakerdeck.com

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 19

I’m disappointed by @cziscience.bsky.social’s decision to discontinue the Science Diversity Leadership Award

chanzuckerberg.com/rfa/science-... no longer exists. But we exist & science needs us❤️‍🔥

👀 previous info at web.archive.org/web/20250130...

I’m among those who had written a Letter of Intent

Supporting Scientific Research to Cure All Diseases

We’re investing in new technology and collaborative research to cure all disease by 2100

chanzuckerberg.com

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 13

After teaching #LCG-UNAM students about these tools, at @libdrstats.bsky.social I talked about "R coding using GitHub Copilot with RStudio and related R packages"

Shoutouts @simonpcouch.com @theotheredgar.bsky.social @hadley.nz et al! #RStats @posit.co

youtu.be/qWuoVQG5BZw

[2025-01-31] R coding using GitHub Copilot with RStudio and related R packages

YouTube video by Leonardo Collado Torres

youtu.be

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Reposted by LIBD rstats club

Louise Huuki-Myers @lahuuki.bsky.social · Feb 14

Check out my journal club presentation on the crumblr pre-print from Hoffman and Roussos, a new method to analyze differential composition in #singlecell data 🍪
Looks very useful for single cell RNA-seq data with case/control study design 🤔
📄 doi.org/10.1101/2025...
▶️ www.youtube.com/watch?v=Hi5E...

Fast, flexible analysis of differences in cellular composition with crumblr

Changes in cell type composition play an important role in human health and disease. Recent advances in single-cell technology have enabled the measurement of cell type composition at increasing cell ...

doi.org

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 13

A few months late, but here's our @libdrstats.bsky.social "End of year GitHub cleanup" 2024 activity guidelines

youtu.be/MrMae8vikGQ

< 5 min video

Thank you all #OpenSource developers who make #RStats and other software we depend on!

[2024-12-13] End of year GitHub cleanup

YouTube video by Leonardo Collado Torres

youtu.be

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jan 28

Congratulations to @soniagr.bsky.social, rytenlab.com team, et al for this project re-analyzing #GTEx human gene expression data uniformly re-processed with #recount3

It was a pleasure working with Sonia G & Mina Ryten

doi.org/10.1038/s414...

@bioconductor.bsky.social @lieberinstitute.bsky.social

Sonia Garcia-Ruiz @soniagr.bsky.social · Jan 27

New in @naturecomms.bsky.social: I'm thrilled to share with you our latest work that applies #srRNAseq to understand splicing accuracy across human introns, tissues and in the context of ageing and neurodegeneration www.nature.com/articles/s41...

Splicing accuracy varies across human introns, tissues, age and disease - Nature Communications

Inaccuracies in RNA splicing may play a significant role in aging and disease. Here, the authors present a comprehensive characterization of splicing accuracy across over 14,000 human samples, offerin...

www.nature.com

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Mariano.sh @mariano-r.bsky.social · Feb 6

¿Hay comunidad #rstats en Bluesky?

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Reposted by LIBD rstats club

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 12

Check our recent video "[2025-01-29] R/Bioconductor-powered Team Data Science: TLDR version 2025"
youtu.be/alL-g2roXxM

We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻

Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...

👥 go.bsky.app/53gy4UP

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Feb 12

We frequently compare RNA-seq t-statistics, so we spent time checking threshold-free methods implemented by Gabriel Hoffman in doi.org/10.1016/j.bi... using #qvalue, plus concordance at the top plots by @rafalab.bsky.social @leviwaldron1.bsky.social

@bioconductor.bsky.social

youtu.be/44RQ7xCXmcQ

[2025-02-05] Comparing DE results using threshold-free methods

YouTube video by Leonardo Collado Torres

youtu.be

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jan 31

Check out this second post by a #LCG-UNAM student on a @bioconductor.bsky.social #rstats package 📦 they were interested in

It's about #scDotPlot by @laufer.bsky.social: we should use at @lieberinstitute.bsky.social @libdrstats.bsky.social for our #scRNA-seq & spatial data!

bsky.app/profile/lcol...

Gabriel Ramírez-Vilchis @gabrielramirezv.bsky.social · Jan 30

Single-cell RNA sequencing is very important when studying gene expression. I found scDotPlot package developed by @laufer.bsky.social, and I think it could be a very useful tool to analyze and plot scRNA-seq data using R.

You can find more information in bioconductor.org/packages/rel...

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