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

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!

🎨 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

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

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

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

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!

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

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

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

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

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...

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...

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

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

🚀 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

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

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

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...

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!

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

¿Hay comunidad #rstats en Bluesky?

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

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

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...

I just copied Marcel Ramos (@mramos148.bsky.social) from @bioconductor.bsky.social core and edited my GitHub profile to display stats thanks to @anuraghazra.bsky.social's excellent github.com/anuraghazra/... raw.githubusercontent.com/LiNk-NY/LiNK... --> github.com/lcolladotor/...

🚀 Sharing insights on ArchR, a powerful tool for single-cell chromatin accessibility analysis! 🎯 ArchR excels in large datasets and integrates scATACseq with scRNAseq for cutting-edge multi-modal studies. 🎥 Dive deeper with the video: youtu.be/XNZx5Dlp6jY?...
 #Bioinformatics #10xGenomics #LIBD

Welcome to #AcademicSky 🦋 Kristen Maynard @kr-maynard.bsky.social!!! Kristen and I have been working closely together since 2019 at @lieberinstitute.bsky.social on #SpatialTranscriptomics projects among other ones. Make sure to follow her to get the latest on her team's preprints and papers! 👀 📜

They can also find relay networks. Like A —> B —> C instead of just A —> B and B —> C. I missed getting a photo of this great slide! The image below is from a previous slide showing how the results from #CellNEST can be visualized 🎨 I’m looking forward to the paper 📜! #SpatialBiology

Registration for posit::conf(2025) just opened. More program details will be gradually rolling out. If you're into 📦 #rstats package development 📦 (or want to be!), check out my workshop.

Thanks everyone for sharing your experiences in our panel today at #SpatialBiology Sean Houghton www.linkedin.com/in/sean-houg... x.com/wcmenglander... Lei Li www.linkedin.com/in/lei-li-46... @leili-bioinfo.bsky.social Gregory Schwartz www.linkedin.com/in/schwartzg... twitter.com/Schwartastic

Ah, "How to name files", a topic that is near and dear to my 💜 My most recent (and semi-polished) iteration on this stuff was a 5-minute lightning talk for NormConf 2022. Here's the video & the slides: youtu.be/ES1LTlnpLMk?... speakerdeck.com/jennybc/how-...

Next we’ll hear from a panel about the future needs of spatial multi-omics I’m guessing that it’ll mostly be about #SpatialTranscriptomics + #SpatialProteomics Though I know that there’s also spatial ATAC and spatial methylation

Today at #SpatialBiology West Coast US 2024 I'll be sharing some of the lessons we've learned since 2019 analyzing 🧐 #Visium & more recently #VisiumHD #SpatialTranscriptomics data 🧬 with my colleagues at @lieberinstitute.bsky.social & @jhubiostat.bsky.social speakerdeck.com/lcolladotor/...

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.

I've completed "Red-Nosed Reports" - Day 2 - Advent of Code 2024 🔴 #AdventOfCode adventofcode.com/2024/day/2

Sign-up for the next round of the rainbowR buddies scheme is open! Buddies will be paired/introduced on Dec 9th 🌈👯‍♂️ If you're LGBTQ+ and code in #RStats, and want an opportunity to connect with someone else in the community (through a random pairing), then this is for you 😃 rainbowr.org/buddies

In a week from now, I'll be at Spatial Biology US West Coast organized by Oxford Global Here's a 2 min pre-event interview by Chloe Donohoe where I talk about why I'm looking forward to attending this conference. Check it out ^^ 👀 oxfordglobal.com/precision-me... youtu.be/Hgzgtvw-sx8

Check this journal club presentation by @nick-eagles.bsky.social on: > #ENACT: End-to-End Analysis of Visium High Definition (HD) Data Nick also compared #ENACT against #bin2cell #VisiumHD @10xgenomics.bsky.social #PyStats 📼 youtu.be/0D6l01ArI9M

Yes indeed - just in a nonlinear setting (needed in single cell genomics for accurate representation).

We made our own manual URL referral website in case we need to update Globus collections which completely remakes the URL Example github.com/LieberInstit... So research.libd.org/globus/jhpce... is the URL on papers that currently points to app.globus.org/file-manager... but we can change as needed

Finally, anything larger that we can’t deposit to NCBI SRA, NCBI GEO, NIMH Data Archive, or similar, we host ourselves through our local cluster and make Globus collections that are publicly available See research.libd.org/globus/

However, we don’t store data on GitHub in general (to avoid using git-lfs “large file storage”) It’s easy to upload zip files to Figshare (within the max 20 GB per file for free). So we do that for supplemental images such as RNAScope) or medium files help.figshare.com/article/figs...

Zenodo has a great integration with GitHub. So we deposit all our code on Zenodo too. docs.github.com/en/repositor... It’s funded by CERN (European Nuclear Research) so it’ll be around a long time en.wikipedia.org/wiki/Zenodo

On the topic of non-negative matrix factorization (NMF, implemented in #RcppML among other #RStats 📦 s) the #NSF paper by Townes & Engelhart citation #7 was great! 💯 (@lahuuki.bsky.social journal club 📹🔜!) www.nature.com/articles/445... published in 1999 shows how NMF gets face elements unlike PCA

I love seeing starter packs for team/institutions members & alumni! ^^ #AcademicSky I just followed all @saezlab.bsky.social 😁 Here’s the one I made for my team bsky.app/profile/lcol... We also have similar ones at @libdrstats.bsky.social @lieberinstitute.bsky.social & @jhubiostat.bsky.social ^^

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you) Also juliosaezrod.bsky.social has recently joined Bluesky go.bsky.app/5ZtPHPz

Last Thursday @nick-eagles.bsky.social presented preliminary exploration results on how to analyze #VisiumHD with open-source software (mostly #RStats & #PyStats) Some of it was designed for #VisiumHD, but some was preexisting We are excited about this new #SpatialTranscriptomics frontier! 🌌 🔭

I'm thrilled to share with you that #visiumStitched led by @nick-eagles.bsky.social has now been published Our #RStats / @bioconductor.bsky.social 📦 provides a framework for stitching together multiple #Visium @10xgenomics.bsky.social capture areas together #AcademicSky doi.org/10.1186/s128...

I'm excited to see that @jhubiostat.bsky.social created a starter pack for members and alumni of this historical department Help us spread the word around to get more members and alumni on it! 🙌🏽 #AcademicSky #Biostats #Biostatistics go.bsky.app/T6DV4MQ