Acรก va en espaรฑol ๐ฒ๐ฝ
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"ยกEstamos orgullosos de anunciar que nuestro artรญculo โAnรกlisis Transcriptรณmico de la Habรฉnula Humana en Esquizofreniaโ es el artรญculo de portada de la ediciรณn de noviembre del American Journal of Psychiatry!" ๐ง #HabenulaLIBD #snRNAseq #Habรฉnula doi.org/10.1176/appi...
05.11.2025 23:47 โ ๐ 8 ๐ 4 ๐ฌ 1 ๐ 1
#OpenData and #OpenCode from our latest @lieberinstitute.bsky.social project
Lots of #RStats and @bioconductor.bsky.social code inside of that repository!
#OpenScience
04.11.2025 22:02 โ ๐ 3 ๐ 2 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-07-11] Tidy manipulation of SingleCellExperiment objects
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
04.11.2025 16:09 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-06-13] Intro to data.table and dtplyr for data manipulation
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
13.06.2025 16:29 โ ๐ 12 ๐ 5 ๐ฌ 0 ๐ 0
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!
09.06.2025 16:10 โ ๐ 4 ๐ 3 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
Choosing a Color Palette
๐จ 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 !
๐ youtu.be/9tAeTjVD7ns
Letโs make our plots both beautiful and accessible!
#RStats @libdrstats.bsky.social
09.06.2025 16:10 โ ๐ 12 ๐ 5 ๐ฌ 1 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-05-30] Reshaping data, Joining tables
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!
๐ฅ youtu.be/5L133h_1SNo
๐ speakerdeck.com/manishabarse...
@libdrstats.bsky.social #DataWrangling #DataScience
06.06.2025 20:38 โ ๐ 7 ๐ 4 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-05-23] Introduction to dplyr for data manipulation
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
06.06.2025 17:36 โ ๐ 10 ๐ 3 ๐ฌ 0 ๐ 0
Redirecting
Learning more about APOE differences in the cell types of the brain ๐ง
I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimerโs disease" from @zhaonaa.bsky.social at our team journal club, check it out!
doi.org/10.1016/j.ne...
โถ๏ธ youtu.be/L4J9jFS-Pic
28.05.2025 18:33 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
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!
28.05.2025 15:07 โ ๐ 3 ๐ 1 ๐ฌ 1 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-04-11] Scaffolding R-Shiny apps with generative AI
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
27.05.2025 21:16 โ ๐ 7 ๐ 5 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-05-02] pseudobulk analysis with pseudoBulkDGE()
Presented at @lieberinstitute.bsky.social #RStats club on pseudobulk analysis using pseudoBulkDGE()๐ A handy wrapper for DE analysis following OSCA guidelines-shared a demo & walked through the method!โจ
๐ฅ youtu.be/0OkWBLyLrfg
๐ speakerdeck.com/manishabarse...
@libdrstats.bsky.social #Bioinformatics
23.05.2025 16:48 โ ๐ 7 ๐ 5 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-04-04] Writing nested array jobs at JHPCE and designing run_all.sh scripts
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
23.05.2025 14:59 โ ๐ 6 ๐ 4 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-04-23] Journal club on "[...] deconvolution of pooled snRNA-seq using sex-dependent gene expr"
Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression๐งฌ
Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach๐
๐ฅ youtu.be/zpeCFwYfV3o
๐ speakerdeck.com/manishabarse
#snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social
22.05.2025 21:51 โ ๐ 8 ๐ 6 ๐ฌ 1 ๐ 1
Deconvolution Benchmark: TL;DR โ Louise A. Huuki-Myers
A high level overview of the Deconvolution Benchmark project, now published in Genome Biology!
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...
11.04.2025 14:34 โ ๐ 9 ๐ 5 ๐ฌ 1 ๐ 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
๐ ๏ธ research.libd.org/DeconvoBuddi...
11.04.2025 14:34 โ ๐ 9 ๐ 5 ๐ฌ 1 ๐ 0
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
14.03.2025 20:11 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
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…
๐ 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!
๐บ Watch here: speakerdeck.com/cyntsc/clust...
๐ Slides: www.youtube.com/watch?v=mE77...
#RStats
13.02.2025 17:40 โ ๐ 8 ๐ 6 ๐ฌ 0 ๐ 0
Supporting Scientific Research to Cure All Diseases
Weโre investing in new technology and collaborative research to cure all disease by 2100
Iโm disappointed by @cziscience.bsky.socialโs decision to discontinue the Science Diversity Leadership Award
chanzuckerberg.com/rfa/science-... no longer exists. But we exist & science needs usโค๏ธโ๐ฅ
๐ previous info at web.archive.org/web/20250130...
Iโm among those who had written a Letter of Intent
19.02.2025 03:23 โ ๐ 22 ๐ 9 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-01-31] R coding using GitHub Copilot with RStudio and related R packages
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
13.02.2025 15:54 โ ๐ 17 ๐ 3 ๐ฌ 1 ๐ 0
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 ...
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 ๐ช
Looks very useful for single cell RNA-seq data with case/control study design ๐ค
๐ doi.org/10.1101/2025...
โถ๏ธ www.youtube.com/watch?v=Hi5E...
14.02.2025 10:23 โ ๐ 8 ๐ 4 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2024-12-13] End of year GitHub cleanup
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!
13.02.2025 15:28 โ ๐ 4 ๐ 2 ๐ฌ 1 ๐ 0
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
28.01.2025 20:54 โ ๐ 10 ๐ 6 ๐ฌ 0 ๐ 0
ยฟHay comunidad #rstats en Bluesky?
06.02.2025 18:01 โ ๐ 6 ๐ 2 ๐ฌ 2 ๐ 0
Highlight image from YouTube
Zoom AI summary screenshot
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 ๐ป
Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...
๐ฅ go.bsky.app/53gy4UP
12.02.2025 21:35 โ ๐ 10 ๐ 5 ๐ฌ 0 ๐ 0
YouTube video by Leonardo Collado Torres
[2025-02-05] Comparing DE results using threshold-free methods
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
12.02.2025 21:49 โ ๐ 8 ๐ 2 ๐ฌ 0 ๐ 0
Check out this second post by a #LCG-UNAM student on a @bioconductor.bsky.social #rstats package ๐ฆ 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...
31.01.2025 20:26 โ ๐ 9 ๐ 5 ๐ฌ 0 ๐ 0
Neuroscience Graduate student in โช
@kr-maynard.bsky.socialโฌ group โชat the @lieberinstitute.bsky.socialโฌ
Unraveling the mysteries of the Locus Coeruleus
Spatial transcriptomics enthusiast
Mapping brain complexity, one dataset at a time!
Researcher in neuroscience and psychiatric genomics, University of Exeter
Investigator Lieber Institute for Brain Development
Assoc. Prof. of Psychiatry @harvardmed.bsky.social
@harvardbrainsci.bsky.social
Director NeuroGenomics & Translational Bioinformatics @McleanHospital
Associate member @broadinstitute.org
https://daskalakislab.mclean.harvard.edu/
Computational Biologist, Head of research @ebi.embl.org, part-time
Heidelberg University, codirector DREAM challenges. For group's activities, see @saezlab.bsky.social
Account of the Saez-Rodriguez lab at EMBL-EBI and Heidelberg University. We integrate #omics data with mechanistic molecular knowledge into #opensource #ML methods
Website: https://saezlab.org/
GitHub: https://github.com/saezlab/
PhD Candidate @CSHL | Genomic Sciences @LCG-UNAM | https://reneegf.github.io/ | she/her | ๐ฒ๐ฝ
Investigator @lieberinstitute.bsky.social/ Associate Professor of Psychiatry and Behavioral Sciences @johnshopkins.bsky.social + Associate Professor of Biological Psychology and Cognitive Neuroscience @UNIBA https://shorturl.at/VVhk5.
Statistician doing genomic data science, faculty the University of Chicago, Korean, Argentinean, American. Love kimchi, math, science, books with beautiful prose.
Ph.D. student, Biostatistics, @jhubiostat.bsky.social
she/her
Website: sparthib.github.io/blog
#rstats ๐ for genomics ๐งฌ ๐ป
views are my own
Biomedical data scientist working at the intersection of machine learning ๐ค, computational omics ๐งฌ, and population health ๐จโ๐ฉโ๐งโ๐ฆ
๐จโ๐ป Incoming assistant professor @University of Utah
๐ Personal website: https://boyi-guo.com/
๐ค Pronounce: he/him
Comms professional. Black Lives Matter. LGBTQ+ ally. Science & medicine are real. Animals are cute.
Computer Scientist | Using transcriptomic data to understand RNA splicing changes in human disease | Research Associate at the @RytenLab #UKDRI Cambridge | But also interested in cats, music and astronomy ๐๐โโฌ๐
I am fascinated by science, it inspires me and keeps me very motivated.
๐ง Staff Scientist at Lieber Institute for Brain Development | ๐ Master in Computer Sciences | ๐ Doctorate in Biological Sciences I Advanced analysis on multiomics and Visium ST
Anesthesia resident, physician scientist
genomics & addiction neurobiology
๐ &๐ฑ dad
Biostats and Human Genomics ๐งฌ๐งฎ.
BS LCG-UNAM ๐ฒ๐ฝ
Researcher at the MRC Biostatistics Unit, University of Cambridge
![[2025-07-11] Tidy manipulation of SingleCellExperiment objects](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:vgwb54dz4sgqmstahrs7w34u/bafkreifcw3sqpzrs6sgu7tnowgvgjrmhg4wcki6gcf73duxpkda42gled4@jpeg)
![[2025-06-13] Intro to data.table and dtplyr for data manipulation](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:vgwb54dz4sgqmstahrs7w34u/bafkreid3dm6kns2smx55ctolfkzci24z5skeibvupqyg5kopjflmayiupq@jpeg)
![[2025-05-30] Reshaping data, Joining tables](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:v776v3myqwukex76bmiivcup/bafkreignuuxbnusvte54l6mv52juae3mjijq4weau3b3dwxfkztuf4twse@jpeg)
![[2025-05-23] Introduction to dplyr for data manipulation](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:vgwb54dz4sgqmstahrs7w34u/bafkreie5x7f2r2omocu7upfm2lg4kwp4vrn3pxswj54ap4c3imq5wy56fe@jpeg)
![[2025-04-11] Scaffolding R-Shiny apps with generative AI](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:xjtki6eywocqeb332tixs6is/bafkreigiscvclblo4dk4vp3fo3rytxuqn7eriem2ipny3m2lfujhw3qt3q@jpeg)
![[2025-05-02] pseudobulk analysis with pseudoBulkDGE()](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:v776v3myqwukex76bmiivcup/bafkreiakm3vzq2de3nqowfckddb3mxe7p24ij4ff5zr3zftqnnvilymgyq@jpeg)
![[2025-04-04] Writing nested array jobs at JHPCE and designing run_all.sh scripts](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:vgwb54dz4sgqmstahrs7w34u/bafkreiest6nwrc7pawuymat6idgw2ekktxjziccjdxrsc5jwi6dda3hsbi@jpeg)
![[2025-04-23] Journal club on "[...] deconvolution of pooled snRNA-seq using sex-dependent gene expr"](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:v776v3myqwukex76bmiivcup/bafkreigox5u4ige36irzgwx3egj37xnlblhqucsbz2sjmcxj6coufs5ife@jpeg)
![[2025-01-31] R coding using GitHub Copilot with RStudio and related R packages](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:h7p2smbyfobkpcs7dbgvhmeh/bafkreib5zjfpgok2bh7gcimdojwgbdsgjjzqqt7wgewc4i2khmhxeulerm@jpeg)
![[2024-12-13] End of year GitHub cleanup](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:h7p2smbyfobkpcs7dbgvhmeh/bafkreihxoiavpam26c4c6fju66zvjhjggylnc23tdmu7rjvghp3mvw3ylm@jpeg)
![[2025-02-05] Comparing DE results using threshold-free methods](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:h7p2smbyfobkpcs7dbgvhmeh/bafkreideoq3f4x33lfh4i6ipmmtfd2ggufu5hnb4kwn7k4hpjyptcf3564@jpeg)
