lcolladotor.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Thanks so much for the fab how-to video!

submitted 2 days ago • 0 comments

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...

submitted 36 days ago • 0 comments

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

submitted 8 days ago • 0 comments

👉 Sharing a talk of the molecular neuroanatomical map of the human prefrontal cortex. This study integrates Visium Spatial data with snRNA-seq to map cell types and interactions across spatial domains. Le Watch here: youtu.be/EhP5-mhw29w Slides on video Explore: research.libd.org/spatialDLPFC/

submitted 17 days ago • 0 comments

New Paper Alert! We report the genome sequence of Eubacterium callanderi AM6, isolated from a Parkinson’s disease patient. This adds to our understanding of gut microbiota in neurodegenerative diseases shorturl.at/pfZwV. This study was done in collaboration with SKAN Research Trust, India

submitted 9 days ago • 0 comments

It's always special to go back to your alms mater. I had a great time with the 20th class of genomics at #LCG #UNAM

submitted 9 days ago • 0 comments

Bluesky is the place for science.

submitted 9 days ago • 83 comments

Wow. "NIH" canceled my co-mentored (with Dave Sulzer) PhD student's F31 funding. His work is on understanding the genetics and neuroscience of language learning disorders. F31 provides no indirect $ to Columbia, just pays his salary. Not that it should matter, but he's an American citizen. W.T.F.

submitted 11 days ago • 20 comments

Today is International Women’s Day! It’s an important day for us (although the R-Ladies mission is not limited to women). 💜Who are we? R-Ladies is a worldwide organization whose mission is to promote gender diversity in the R community.

submitted 14 days ago • 2 comments

New blog post: "Teaching #omics #methods to #LCG-UNAM students" Thanks for inviting me @vaalarias.bsky.social and Dr Constance Auvynet ^_^ Blog post is available in both English and Spanish 🇲🇽 #genomics #scRNAseq #Visium #spatialomics @10xgenomics.bsky.social lcolladotor.github.io/2025/03/07/t...

submitted 15 days ago • 0 comments

Check this blog pst by @rafalab.bsky.social explaining indirect cost at US research institutions and what they pay for simplystatistics.org/posts/2025-0... #AcademicSky

submitted 26 days ago • 1 comment

Probably worth downloading Notices of Grant Awards or anything else you’d like to keep a permanent record of from ERA Commons.

submitted 28 days ago • 2 comments

I want to see every scientific society going into emergency mode. This is a good example of how an organization can flex its specific power in a time of great need. What else is possible?

submitted 28 days ago • 6 comments

Updated from the preprint, our paper, "Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation" is now published. www.cell.com/cell-reports...

submitted 29 days ago • 4 comments

For #FluorescenceFriday - Optimizing some labeling in prep for piloting some high resolution, circuit spatial transcriptomics that I could not be more excited about!! Kudos to RA Madeline Abramson and @rphillips3.bsky.social for pushing these experiments forward 🧠🔬🧪👩‍🔬

submitted 29 days ago • 2 comments

Thrilled to share my 1st PhD's 1st publication at @liigh-unam.bsky.social. Anecdotally it is also my 1st paper as corresponding author from my group / the "Paloegenomics and Evolutionary Biology". shorturl.at/VumOq Let us know what you think about it.

submitted 30 days ago • 1 comment

🚀 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

submitted 37 days ago • 0 comments

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

submitted 32 days ago • 0 comments

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

submitted 37 days ago • 1 comment

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!

submitted 37 days ago • 1 comment

🧬 Unlock the Power of Metabolic Networks with MetaDAG! 🚀 OUR NEW PAPER IS OUT!! rdcu.be/d7RJF MetaDAG is a web-based tool designed to simplify metabolic network reconstruction and analysis. #MetabolicNetworks #OmicsData #Bioinformatics #KEGG #DataAnalysis #MetaDAG #ScienceTool #BigData

submitted 52 days ago • 1 comment

Need to export references from #SciWheel? In this <2 min video I show you how to do so. You can export them to #BibTeX, #CSV, or #RIS files which can be imported in other reference management software. youtu.be/1ZjHBxTVtk4 #AcademicSky

submitted 38 days ago • 0 comments

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

submitted 38 days ago • 0 comments

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

submitted 38 days ago • 0 comments

🧵 The Fight Has Come to Them: Science, Institutions & The Indirects Cut I want to take a moment to talk about the perspective behind these slides I put together. I’ve framed them to be as nonpartisan as possible—but in a moment this polarized, there are limits here. 1/

submitted 40 days ago • 1 comment

Made some slides for scientists to talk about what's been happening & what we should do next. There are probably many people better qualified than me to talk about these issues. If that's you, please, please, please consider holding some virtual advocacy training sessions for researchers this week.

submitted 40 days ago • 18 comments

On changes to #NIH indirect rates, there is a law in place that prohibits NIH from making such changes without the approval of Congress. See Division D, Title II Section 224 of The Further Consolidated Appropriations Act, 2024 (Public Law No: 118-47) grants.nih.gov/grants/guide...

submitted 43 days ago • 81 comments

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...

submitted 43 days ago • 269 comments

Feeling ready for the @jhubiostat.bsky.social BSO (Biostats Student Org) Cultural Potluck! 🗺️ It's great to see current students re-implement the Cultural Mixers @mandymejia.bsky.social & I ran in 2012-~2015 lcolladotor.github.io/2013/11/20/s... 📸 with @mgschiavon.bsky.social @surh.bsky.social

submitted 43 days ago • 0 comments

#GEOquery is a @bioconductor.bsky.social package that allows us to acquire data from NCBI's Gene Expression Omnibus, which is why we should be thankful to @seandavi.bsky.social for keeping it up to date. For more details, visit: bioconductor.org/packages/3.2...

submitted 43 days ago • 2 comments

curatedTCGAData is an R package available on Bioconductor that provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. You can find more information at: bioconductor.org/packages/release/data/experiment/html/curatedTCGAData.html.

submitted 46 days ago • 0 comments

Hi!👋 I recently came across #CatsCradle, a @bioconductor.bsky.social package developed by Anna Laddach and Michael Shapiro that provides powerful methods for analyzing spatial transcriptomics data and discovering gene clusters. 💻🐈‍⬛ For more information: 🔗 bioconductor.org/packages/rel...

submitted 46 days ago • 0 comments

I explored simona from @bioconductor.bsky.social , an amazing tool for analyzing biological ontologies 🧬. With more than 70 semantic similarity analysis methods, simona is a robust tool for bioinformatics research. 🌟 For more information www.bioconductor.org/packages/rel...

submitted 46 days ago • 0 comments

I checked out scoup from @bioconductor.bsky.social, a tool for simulating codon sequences under Darwinian selection 🧬. Great for fitness landscapes & evolutionary studies! 🌍🔬 More info here: bit.ly/3PZtbTj #Evolution #Bioinformatics #CodonSim #Rstats

submitted 49 days ago • 0 comments

I explored scDotPlot from @bioconductor.bsky.social, an amazing tool for generating dot plots with scRNA-seq data 📊. It supports hierarchical clustering and works seamlessly with Seurat and SingleCellExperiment objects. 🧬 Details: bit.ly/3EhQO6Z #scRNAseq #Bioinformatics #DataVisualization

submitted 49 days ago • 2 comments

Thank very much @freneegf.bsky.social for teaching #LCG-UNAM students how to make their own websites with: * RStudio project + * Git repo + * GitHub website using the #postcards #rstats 📦 by @seankross.com It's been great to be part of your academic journey! lcolladotor.github.io/rnaseq_LCG-U...

submitted 50 days ago • 0 comments

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...

submitted 50 days ago • 0 comments

Check out his post by a LCG-UNAM student on the #immunogenViewer @bioconductor.bsky.social #rstats package 📦 During my class (lcolladotor.github.io/rnaseq_LCG-U...) they learned how to check the Bioconductor release notes and find 📦s that they might be interested in bioconductor.org/news/bioc_3_...

submitted 50 days ago • 0 comments

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...

submitted 52 days ago • 1 comment

immunogenViewer package for R, developed by Katharina Waury, seems to be such a good way to analyze proteins in order to find targets for some antibodies! You can find it in bioconductor.org/packages/rel...

submitted 52 days ago • 0 comments