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Reposted

Ming Tommy Tang @tommytang.bsky.social · 7d

Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data www.nature.com/articles/s4...

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Reposted

Waggoner Lab @labwaggoner.bsky.social · 9d

Neuron-reactive KIR+CD8+ T cells display an encephalitogenic transcriptional program in autoimmune encephalitis @natcomms.nature.com
www.nature.com/articles/s41...

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mheming.bsky.social @mheming.bsky.social · 16d

Do you use agent mode? Because then copilot often corrects itself. I often write some code using the package I want, e.g. Seurat. And then prompt e.g. Write functions to read in all other samples, don t repeat yourself. That works quite well. Sometimes needs a second prompt.

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Reposted

Waggoner Lab @labwaggoner.bsky.social · 20d

A population of anti-CD20–resistant dural B cells that remain in the mouse brain parenchyma at disease remission in progressive multiple sclerosis @jengommerman.bsky.social @jem.org
rupress.org/jem/article-...

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Reposted

Joe Sabatino @jsabatino37.bsky.social · 21d

2024 MS McDonald criteria now published

www.thelancet.com/journals/lan...

www.thelancet.com

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Reposted

Emily Riederer @emilyriederer.bsky.social · 24d

Really insightful post from Julie Tibshirani (spotted in LinkedIn, can't find on Bsky) reflecting on #rstats 's unique governance structure and what can be learned for other languages

jtibs.substack.com/p/if-all-the...

If all the world were a monorepo

The R ecosystem and the case for extreme empathy in software maintenance

jtibs.substack.com

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Reposted

sarah @sarahjohnson.io · Aug 21

I was loving Claude Code... until I tried it with #rstats. Constant errors, wouldn't use the tidyverse even when asked, "optimized" functions were slower.

Frustrated, I started a session just to teach R to Claude and summarize what it learned into a CLAUDE.md file gist.github.com/sj-io/3828d6...

Claude R Tidyverse Expert

Claude R Tidyverse Expert. GitHub Gist: instantly share code, notes, and snippets.

gist.github.com

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Reposted

Visual Studio Code @vscode.dev · 27d

🚀 v1.104 of VS Code is here! Check out what's new:

🤖 Improved coding agent integration
📄 AGENTS.md file support for better context
🔍 New Auto mode (Preview) for smart model selection
🔑 Model flexibility via BYOK extension API

…and more: aka.ms/VSCodeRelease

Here are the highlights 🧵

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Reposted

Thomas Lin Pedersen @thomasp85.com · 27d

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

ggplot2 4.0.0

A new major version of ggplot2 has been released on CRAN. Find out what is new here.

www.tidyverse.org

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Reposted

Ming Tommy Tang @tommytang.bsky.social · Sep 8

23 tools to work with (single-cell) TCR/BCR-seq immune repertoire data 🧵 👇

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mheming.bsky.social @mheming.bsky.social · Sep 7

You should include quarto, which also includes python and julia and includes bookdown, blog down etc per se

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mheming.bsky.social @mheming.bsky.social · Sep 1

Very cool. Habe you tried Kinesis Advantage before for a direct comparison? Voyager looks stylisher, although Kinesis has this "bowl" area and more keys in the thumb cluster (which i like for Alt, Ctrl, Super, Alt-Gr, Space, Backspace) .. voyager looks better for a voyage :)

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mheming.bsky.social @mheming.bsky.social · Sep 1

Nice. Which keyboard is that? I am quite happy with kinesis advantage but that one looks also comfortable.

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Reposted

Ted Price @tedpricethepainguy.bsky.social · Aug 24

BOOM! Cool to see the final form of this great work now published. Deep new insight into human peripheral neuropathy. Congrats @mheming.bsky.social and colleagues on a great study.

mheming.bsky.social @mheming.bsky.social · Aug 24

Very proud that our human PNS atlas is finally published in @natcomms.nature.com We found perineurial hyperplasia and lipid-associated nerve macrophages in #polyneuropathies.
Explore: pns-atlas.mzhlab.com
A tweetorial 1/13
doi.org/10.1038/s414...

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Reposted

Ted Price @tedpricethepainguy.bsky.social · Aug 24

Very impressed with this finding which is quite similar to what we have also seen in DPN nerves. Suggests a completely different disease modifying approach for multiple types of peripheral neuropathy.

mheming.bsky.social @mheming.bsky.social · Aug 24

12/13
PNPs showed previously unknown perineurial hyperplasia and fibrotic dispersion and this was most pronounced in immune-mediated PNPs.

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mheming.bsky.social @mheming.bsky.social · Aug 24

Linking people who were involved or who might be interested in reading this:
@mzhlab.bsky.social @clsommer25.bsky.social
@tommytang.bsky.social @tedpricethepainguy.bsky.social @denklab.bsky.social

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mheming.bsky.social @mheming.bsky.social · Aug 24

13/13 Validated in a larger cohort (370 fascicles; 18 CTRL, 12 CIDP): manual perineurium measurements. Linear mixed model (age+sex fixed, center/sample random) showed perineurial area & perimeter increased in CIDP.

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mheming.bsky.social @mheming.bsky.social · Aug 24

12/13
PNPs showed previously unknown perineurial hyperplasia and fibrotic dispersion and this was most pronounced in immune-mediated PNPs.

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mheming.bsky.social @mheming.bsky.social · Aug 24

11/13 Transcriptional changes affected multiple cells outside of the endoneurium across PNPs, suggesting PNPs as pan-nerve diseases (using miloDE)

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mheming.bsky.social @mheming.bsky.social · Aug 24

10/13 immune, repairSC and periC3 cluster also correlated with clinical disease severity (INCAT score) and myelin thickness (g-ratio). (using CNA @ilyakorsunsky.bsky.social

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mheming.bsky.social @mheming.bsky.social · Aug 24

9/13 LAM markers (SPP1/osteopontin, PLIN2, CD36, FABP5) colocalized histologically with myelin and BODIPY (labels neutral lipids). LAM thus likely has myelin-phagocytizing capacity.

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mheming.bsky.social @mheming.bsky.social · Aug 24

8/13 PNPs shared an increase in endoneurial lipid-associated macrophages (LAM).

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mheming.bsky.social @mheming.bsky.social · Aug 24

7/13 Human peripheral nerves contained complex immune cells, including a plethora of myeloid cell populations. Macrophage clusters exhibited an endoneurial to epineurial gradient, previously described in rodents.

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mheming.bsky.social @mheming.bsky.social · Aug 24

6/13 Integrating spatial transcriptomics with snRNA-seq provided an unbiased histological annotation of peripheral nerve cells.

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mheming.bsky.social @mheming.bsky.social · Aug 24

5/13 We identified novel and human-specific nerve cell type markers using snRNA-seq, which were validated using spatial transcriptomics

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