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libdrstats.bsky.social
LIBD rstats club
@libdrstats.bsky.social
240 followers 91 following 13 posts
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/
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libdrstats.bsky.social
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
Reposted by LIBD rstats club
nick-eagles.bsky.social
Hot take: ggplot2 is better than any plotting option available in Python-- but I discuss a couple options in Python at an R Stats Club session @libdrstats.bsky.social linked below. I personally use plotnine, since it's essentially a port of ggplot2 for Python.

youtu.be/xK9UNcOfjnI
[2025-07-18] Plots in Python with seaborn and plotnine
YouTube video by Leonardo Collado Torres
youtu.be
November 13, 2025 at 3:02 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
Nuestros datos de #Habénula y de expresión diferencial pueden ser explorados vía sitios web interactivos 💻 #DatosLibres #iSEE 👀

github.com/LieberInstit...
GitHub - LieberInstitute/Habenula_Pilot: habenulaPilot project code repository
habenulaPilot project code repository. Contribute to LieberInstitute/Habenula_Pilot development by creating an account on GitHub.
github.com
November 5, 2025 at 11:47 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
Acá va en español 🇲🇽
--- o ---

"¡Estamos orgullosos de anunciar que nuestro artículo ‘Análisis Transcriptómico de la Habénula Humana en Esquizofrenia’ es el artículo de portada de la edición de noviembre del American Journal of Psychiatry!" 🧠 #HabenulaLIBD #snRNAseq #Habénula doi.org/10.1176/appi...
November 5, 2025 at 11:47 PM
libdrstats.bsky.social
#OpenData and #OpenCode from our latest @lieberinstitute.bsky.social project

Lots of #RStats and @bioconductor.bsky.social code inside of that repository!

#OpenScience
November 4, 2025 at 10:02 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...
Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry
Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...
doi.org
November 4, 2025 at 9:31 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
We recently checked out tidySingleCellExperiment at the R Stats Club @libdrstats.bsky.social, an R package part of a broader effort to bring tidy coding to genomics. Pretty useful!

youtu.be/ob_SQY4-YjQ?...

#RStats
[2025-07-11] Tidy manipulation of SingleCellExperiment objects
YouTube video by Leonardo Collado Torres
youtu.be
November 4, 2025 at 4:09 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
June 13, 2025 at 4:29 PM
Reposted by LIBD rstats club
heenadivecha.bsky.social
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!
June 9, 2025 at 4:10 PM
Reposted by LIBD rstats club
heenadivecha.bsky.social
🎨 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
June 9, 2025 at 4:10 PM
Reposted by LIBD rstats club
mbarse.bsky.social
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
June 6, 2025 at 8:38 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
June 6, 2025 at 5:36 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
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
May 28, 2025 at 6:33 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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!
May 28, 2025 at 3:07 PM
Reposted by LIBD rstats club
geopertea.bsky.social
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
May 27, 2025 at 9:16 PM
Reposted by LIBD rstats club
mbarse.bsky.social
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
May 23, 2025 at 4:48 PM
Reposted by LIBD rstats club
nick-eagles.bsky.social
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
May 23, 2025 at 2:59 PM
Reposted by LIBD rstats club
mbarse.bsky.social
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
May 22, 2025 at 9:51 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
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
April 11, 2025 at 2:35 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
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...
April 11, 2025 at 2:35 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
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
April 11, 2025 at 2:35 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
March 14, 2025 at 8:11 PM
Reposted by LIBD rstats club
cynthiasc.bsky.social
🚀 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
February 13, 2025 at 5:40 PM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
February 19, 2025 at 3:23 AM
Reposted by LIBD rstats club
lcolladotor.bsky.social
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
February 13, 2025 at 3:54 PM
Reposted by LIBD rstats club
lahuuki.bsky.social
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
February 14, 2025 at 10:23 AM