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mheming.bsky.social

@mheming.bsky.social
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Kilian Schober @kischober.bsky.social · 02/10/2026
New preprint from our lab, now on bioRxiv! We are VERY excited about this one! www.biorxiv.org/content/10.6... How does Epstein–Barr virus (EBV) immunity become linked to multiple sclerosis (MS)? (1/8)
biorxiv.org
A pro-inflammatory effector-memory T cell program links peripheral EBV priming to CNS autoimmunity
T and B cell-mediated immunosurveillance of the central nervous system (CNS) can become maladaptive in multiple sclerosis (MS). Epstein-Barr virus (EBV) is a likely driver of MS, yet how exactly EBV-s...
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Ted Price @tedpricethepainguy.bsky.social · 16/09/2026
I am thrilled to announce that we have a new computational neuroscience position available in our Department of Neuroscience and Center for Advanced Pain Studies: jobs.utdallas.edu/postings/32726
jobs.utdallas.edu
Open Rank Tenure Track Faculty Position (Assistant or Associate Professor) in Computational Neuroscience with a focus on Pain and/or Peripheral Neuropathy
Position Description The Department of Neuroscience at The University of Texas at Dallas seeks to hire a tenure-track faculty member with expertise in transcriptomics and/or proteomics, neural computa...
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Gabor Csardi @gaborcsardi.org · 14/09/2026
New beta of #Rstats rig: LOTS of EXCITING stuff: - new: web site: rig.r-lib.org - new: user-mode R installation: rig.r-lib.org/admin-vs-use... - new: manage R packages (CRAN + git): rig.r-lib.org/pkg-guide.html - new: manage R projects and virtual environments: rig.r-lib.org/proj-guide.h...
rig.r-lib.org
rig – the R Installation Manager – rig
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Joe Sabatino @jsabatino37.bsky.social · 11/09/2026
Multimodal discovery of a pathogenic B cell-dependent T cell state in multiple sclerosis academic.oup.com/brain/advanc...
academic.oup.com
Multimodal discovery of a pathogenic B cell-dependent T cell state in multiple sclerosis
Farooq et al. show that B cell depletion in multiple sclerosis indirectly disrupts a proinflammatory-cytotoxic T cell state. Convergent evidence across dis
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Joe Sabatino @jsabatino37.bsky.social · 08/09/2026
Intestinal infections establish antigen-specific, long-lived memory CD4+ T cells in the brain and meninges www.nature.com/articles/s41...
nature.com
Intestinal infections establish antigen-specific, long-lived memory CD4+ T cells in the brain and meninges - Nature Neuroscience
Intestinal CD4+ T cells migrate to the dura and brain following gut infection with bacteria or parasites, establishing a long-lived memory population capable of proliferation and cytokine production f...
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mheming.bsky.social @mheming.bsky.social · 19/08/2026
🚨 We’re hiring! PhD position in **computational biology, single-cell & spatial transcriptomics, and neuroimmunology** at @UKMuenster. Join our team and study immune mechanisms at brain borders & peripheral nerves. 🧠🧬 Apply here 👇 jobs-sf.ukmuenster.de/job/UKM-PHDD... :::
jobs-sf.ukmuenster.de
PHD/Department of Neurology/BBIM/DM/MH
PHD/Department of Neurology/BBIM/DM/MH
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Arc Institute @arcinstitute.org · 17/08/2026
Four years ago, a mystery case led Core Investigator @jvpluv to discover a new diagnosis (ABCD). Today his team published one of the largest clinical surveys of unexplained spinal cord disease to date in @JAMANeuro, finding ABCD in roughly half of patients.
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Waggoner Lab @labwaggoner.bsky.social · 01/07/2026
Blood cytotoxic NK-like CD8 + CD94+ T cells migrate to the brain and predict multiple sclerosis severity academic.oup.com/brain/advanc...
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Peter Dalgaard @pdalgd.bsky.social · 24/06/2026
R version 4.6.1 "Happy Hop" (source version) has been released. It should be on CRAN by now (update of manuals pending). #rstats
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Ming Tommy Tang @tommytang.bsky.social · 17/06/2026
barbieQ: an R software package for analysing barcode count data from clonal tracking experiments academic.oup.com/bioinformat...
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Luciano Martelotto @lgmartelotto.bsky.social · 16/06/2026
3D multi-omics tumour atlases: from technology to biology and clinical translation www.nature.com/articles/s41...
nature.com
3D multi-omics tumour atlases: from technology to biology and clinical translation - Nature Reviews Cancer
In this Review, Liu et al. describe the established and emerging tools for the generation of comprehensive 3D tumour atlases, the analysis of which has the potential to uncover novel biomarkers for ri...
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Ming Tommy Tang @tommytang.bsky.social · 13/06/2026
10/ That’s where Marimo comes in. A new tool that fixes Jupyter’s two biggest flaws: Git diff hell Execution chaos github.com/marimo-team...
github.com
GitHub - marimo-team/marimo: A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.
A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor. - marimo-team/marimo
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mheming.bsky.social @mheming.bsky.social · 07/06/2026
Fixed my Kinesis Advantage 1 choking on Linux kernels for the last few years. If you're on @nixos.org , add this to your config: boot.kernelParams = [ "usbcore.quirks=05f3:0081:mnc,05f3:0007:mnc" "usbcore.old_scheme_first=1" ];
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Bruno Rodrigues @brodriguesco.bsky.social · 23/05/2026
and the video is up now: www.youtube.com/watch?v=wkjL...
youtube.com
Bruno Rodrigues: Reproducible Data Science with Nix
YouTube video by R in Pharma
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Roman Sankowski @rsankowski.bsky.social · 21/05/2026
Like macrophages in general, Lipid-associated “foamy” 🚿macrophages come in different flavors. Here a new story on these big beauties in #multipleSclerosis Foamy microglia link oxylipins to disease progression in multiple sclerosis | @natneuro.nature.com www.nature.com/articles/s41...
nature.com
Foamy microglia link oxylipins to disease progression in multiple sclerosis - Nature Neuroscience
Foamy microglia are associated with multiple sclerosis progression, linking phagocytosis, altered lipid metabolism (oxylipins) and lysosomal stress to nonclassical neuroinflammation and disease severi...
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Ming Tommy Tang @tommytang.bsky.social · 01/05/2026
My talk slides at the Nextflow Summit on reproducible bioinformatics is here divingintogeneticsandgenomics.com/files/slide...
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Peter Dalgaard @pdalgd.bsky.social · 24/04/2026
R version 4.6.0 "Because it was There" (source version) has been released. It should be on CRAN by now. #rstats The choice of codename is in remembrance of R Core member Tomàš Kalibera (1978-2026). Among many other things, he was a keen mountain climber.
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Jumping Rivers @jumpingrivers.com · 21/04/2026
R 4.6.0 "Because it was There" is set for release on 24 April. @russhyde.bsky.social writes up the more interesting changes — %notin% in base R, neater character column summaries, and more. Full breakdown with code: www.jumpingrivers.com/blog/whats-n... #rstats #datascience #rprogramming
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Tyler Morgan-Wall @tylermw.com · 03/04/2026
Introducing 🌳tarborist: a VS Code extension providing tree-sitter powered static analysis of {targets} pipelines with target info on hover, tar_map() autocompletion, cycle detection, and upstream/downstream info/links #RStats Github: github.com/tylermorganw... OpenVSX: open-vsx.org/vscode/item?...
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Maëlle Salmon @masalmon.eu · 02/04/2026
New post on the @ropensci.org blog, "A Better R Programming Experience Thanks to Tree-sitter" Edited by @etiennebacher.bsky.social, @davisvaughan.bsky.social, Steffi LaZerte ropensci.org/blog/2026/04... #RStats
ropensci.org
A Better R Programming Experience Thanks to Tree-sitter
Modern tooling for parsing, searching, formatting, editing R code, just like for other programming languages.
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mheming.bsky.social @mheming.bsky.social · 27/03/2026
@tommytang.bsky.social have you tried opencode? Shouldn t we try to prefer the open source variant? And if you connect it with sonnet/opus I found it very powerful.
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Etienne Bacher @etiennebacher.bsky.social · 24/03/2026
#rstats I'm glad to announce Jarl 0.5.0! Jarl is a very fast R linter, written in Rust. This release brings many improvements and fixes. See the blog post: www.etiennebacher.com/posts/2026-0... And the full changelog: jarl.etiennebacher.com/changelog 🧵 to highlight some features below (1/4)
etiennebacher.com
Jarl 0.5.0
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Ming Tommy Tang @tommytang.bsky.social · 18/03/2026
Most statistical tests you learned separately are the same thing. t-test, ANOVA, Mann-Whitney, Chi-square, Wilcoxon... all just special cases of linear models. y = b0 + b1*x covers almost everything.
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Ming Tommy Tang @tommytang.bsky.social · 11/03/2026
Boris Cherny created Claude Code. Then he open-sourced his entire setup for using it. Memory files, subagents, skills, the whole thing. Here's what's inside and why you should steal it:
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Ming Tommy Tang @tommytang.bsky.social · 07/03/2026
7 FREE Books to learn data science 🧵 👇 (not just bookmark, do read them) 1. Data science: A first introduction datasciencebook.ca/
datasciencebook.ca
Data Science
This is a textbook for teaching a first introduction to data science.
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Isabella Velásquez @ivelasq3.bsky.social · 03/03/2026
I rounded up a few Claude Skills for #RStats users. Huge thanks to the creators who developed them. They share Skills for everything from tidyverse code to brand.yml files to learning while using AI. Hope the list is useful, and please let me know what I missed! 🧡 rworks.dev/posts/claude...
rworks.dev
A Few Claude Skills for R Users – R Works
The community has come together to create some great Claude Skills that you can try out today.
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mheming.bsky.social @mheming.bsky.social · 28/02/2026
@mingemi.bsky.social have you tried opencode with github copilot? if you are a teacher/student you get 300 premium prompts (e.g. claude sonnet 4.6, or 100opus 4.6) for free, which should be similar to claude code (17 or even 100 Dollars). For me that works great although i haven't tried cc yet
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Ming Tommy Tang @tommytang.bsky.social · 27/02/2026
10 websites for drawing scientific figures 👇
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Roman Sankowski @rsankowski.bsky.social · 16/02/2026
Base barrier cells provide compartmentalization of choroid plexus, brain and CSF | Nature Neuroscience www.nature.com/articles/s41...
nature.com
Base barrier cells provide compartmentalization of choroid plexus, brain and CSF - Nature Neuroscience
Verhaege et al. identify a conserved fibroblast barrier population at the base of the choroid plexus that compartmentalizes brain–CSF interfaces and is disrupted by inflammation, revealing a new site ...
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Joe Sabatino @jsabatino37.bsky.social · 05/02/2026
Overjoyed to share our new work exploring the antigen specificity of CSF-expanded CD8+ T cells in #multiplesclerosis #EBV in @natimmunol.nature.com #immunology 🧪🧵1/ www.nature.com/articles/s41...
nature.com
Antigen specificity of clonally enriched CD8+ T cells in multiple sclerosis - Nature Immunology
Sabatino and colleagues examine expanded CD8+ T cell clonotypes from a small cohort of multiple sclerosis patients. They identified several cognate peptide epitopes that derive from Epstein–Barr virus...
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Bruno Rodrigues @brodriguesco.bsky.social · 16/01/2026
#RStats📦rix 0.17.4 is out! Major #Python QoL improvements: automatic LD_LIBRARY_PATH setup for easy integration with uv, new py_src_dir for editable-style Python dev in #Nix shells, and smarter cachix detection (no more noise on #NixOS). Plus docs cleanup & cache setup updates
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Bruno Rodrigues @brodriguesco.bsky.social · 11/01/2026
Reproducible Polyglot Data Science still a WIP, but I think there's already quite a lot of useful content. Will stay free forever: reproducible-data-science.dev buy me an espresso to show your support: buymeacoffee.com/brodriguesco
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mheming.bsky.social @mheming.bsky.social · 04/01/2026
2/2 Using BH/Bonferroni often leaves proteomics (Olink) results underpowered in my analysis, even when scRNA-seq produces plenty of DEGs. Findings (my interpretation): qvalue and permFDP provide higher sensitivity with only a marginal hit to specificity.
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mheming.bsky.social @mheming.bsky.social · 04/01/2026
1/2 For those working on multiple test correction in #Omics: repo: github.com/mihem/compar... result: www.mheming.com/compareFDP/ I’ve tried to benchmark BH against qvalue and permFDP. @tommytang.bsky.social
mheming.com
Comparing False Discovery Proportion (FDP) Methods
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mheming.bsky.social @mheming.bsky.social · 03/01/2026
@tommytang.bsky.social I think you should add permFDP pubmed.ncbi.nlm.nih.gov/36693222/ . I found it very useful in my analysis. I recently tried to make the package more robust github.com/mihem/permFD...
github.com
GitHub - mihem/permFDP at gh_actions
An R package for correcting p-values for multiple hypothesis testing in comparative quantitative omics experiments using permutation-based FDP estimation. - GitHub - mihem/permFDP at gh_actions
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mheming.bsky.social @mheming.bsky.social · 01/01/2026
@tommytang.bsky.social it works for me on my PC but not on my smartphone.
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mheming.bsky.social @mheming.bsky.social · 30/12/2025
@tommytang.bsky.social nice. However if I change to R , loading the R environment crashes chatomics-labs.base44.app/TutorialView... SE for other tutorials
chatomics-labs.base44.app
Chatomics Labs
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John Lukens @lukensjohnr.bsky.social · 29/12/2025
Remodeling of skull bone channels regulates immune infiltration into the meninges during neuroinflammation: Immunity www.cell.com/immunity/ful...
cell.com
Remodeling of skull bone channels regulates immune infiltration into the meninges during neuroinflammation
Skull marrow communicates with the meninges through bone channels, yet their formation and regulation remain poorly understood. Eme-Scolan et al. show that these channels undergo active remodeling dur...
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mheming.bsky.social @mheming.bsky.social · 23/12/2025
Imo this package is a hidden gem. 💎 I’m no statistician, but the logic is solid. With many variables, I got different results than BH—it seems to find signals that standard corrections miss github.com/steven-shuke... @tommytang.bsky.social @brodriguesco.bsky.social what do you think?
github.com
GitHub - steven-shuken/permFDP: An R package for correcting p-values for multiple hypothesis testing in comparative quantitative omics experiments using permutation-based FDP estimation.
An R package for correcting p-values for multiple hypothesis testing in comparative quantitative omics experiments using permutation-based FDP estimation. - steven-shuken/permFDP
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mheming.bsky.social @mheming.bsky.social · 19/12/2025
Nice video, and wow you build that fast. We usually write a manuscript with Google Docs, so we can even work in parallel, I can use citation manager in there etc. What advantage does korppi offer?
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Ming Tommy Tang @tommytang.bsky.social · 16/12/2025
Depending on your data type, use the right plot to tell the story. A nice interactive app to determine what plots you need www.data-to-viz.com/
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Etienne Bacher @etiennebacher.bsky.social · 20/11/2025
#rstats Please welcome Jarl, a new R linter. Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds. Jarl provides several output formats, a Github Actions workflow, and more. Blog post: www.etiennebacher.com/posts/2025-1...
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Jenny Bryan @jennybryan.bsky.social · 12/11/2025
This gives a fantastic framing of how to think about reproducibility (it's a spectrum) and how to use renv with intention. Highly recommend, even if you're not using renv, to get a better understanding of how to live in peace as R and package versions advance 🕊️ #rstats
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Visual Studio Code @vscode.dev · 12/11/2025
Announcing Agent HQ in VS Code: a unified agent experience directly in the editor. Here's what that looks like...🧵
A slide titled “Visual Studio Code – October Update [1.106]” with three columns of feature highlights.

Agent HQ: Agent Sessions view as mission control for agent tasks, OpenAI Codex integration, built-in planning agent, custom agents and handoffs, inlined terminal panels in chat.
Security & Trust: Open sourcing inline suggestions, tool pre- and post-approval, expanded MCP auth support, control MCP server access with custom MCP registries, Linux device policy support.
Great coding experience: Copy text from deleted lines in diff editor, VS Code product icon refresh, Terminal IntelliSense GA, compare source control branches and tags.
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Luciano Martelotto @lgmartelotto.bsky.social · 12/11/2025
www.nature.com/articles/s41...
nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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mzhlab.bsky.social @mzhlab.bsky.social · 05/11/2025
Are you looking for a PhD student position in Münster focussing on neuro-immunology of peripheral nerves? Apply jobs-sf.ukmuenster.de/job/UKM-PhD-...
jobs-sf.ukmuenster.de
PhD Student (gn*) in Peripheral Nerve Neurobiology / Neuro-Immunology
PhD Student (gn*) in Peripheral Nerve Neurobiology / Neuro-Immunology
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Peter Dalgaard @pdalgd.bsky.social · 31/10/2025
R version 4.5.2 "[Not] Part in a Rumble" (source version) has been released. (You can find it in cran.r-project.org/src/base/R-4/, or wait for CRAN to be updated.)
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mheming.bsky.social @mheming.bsky.social · 24/10/2025
And what's your opinion on vs code with R vs positron? Tried positron a year and missed a few things including copilot and remote ssh, which is now available. But not sure it is as good.
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Bruno Rodrigues @brodriguesco.bsky.social · 22/10/2025
if someone wants to give feedback on a paper i’ll be submitting soon titled "Nix for Polyglot, Reproducible Data Science Workflows" that’d be greatly appreciated! github.com/b-rodrigues/...
github.com
rix_paper/paper.qmd at master · b-rodrigues/rix_paper
Contribute to b-rodrigues/rix_paper development by creating an account on GitHub.
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mheming.bsky.social @mheming.bsky.social · 22/10/2025
Or maybe just vs code with r extension, Claude sonnet agent with GitHub copilot . Works great for me.
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