Pierre-Paul Axisa

definitely a problem when dealing with diverse object structures. And you rely on the dev having generated (and documented!) those accessors. I feel like often there’s an "exotic" slot that was deemed unimportant so you have no choice but to @. S4 feels a bit like "don’t do this at home" to me 😅

Seurat versions? · Issue #15 · LTLA/scRNAseq If I convert the datasets present in this package to Seurat format, with metadata retained between versions, would the authors allow a pull request? I know the community is somewhat split over Sing...

The first time I got familiar with this is this epic rant from Aaron Lun on the Seurat R package to analyse single cell RNAseq data: github.com/LTLA/scRNAse...

a man in a military uniform is standing in front of a group of people and says `` right to jail '' . ALT: a man in a military uniform is standing in front of a group of people and says `` right to jail '' .

Definitely illegal

a man with his eyes closed looks at the camera ALT: a man with his eyes closed looks at the camera

And the accessors

a man in a plaid shirt says no no no no wait wait wait wait wait . ALT: a man in a plaid shirt says no no no no wait wait wait wait wait .

S4 methods developers when you type @ to access some slots. #rstats

The closure who loved me

Have you looked at the data? Me:

I feel like we could collectively come up with some great bond flick names re: #rstats, #GitHub, etc 😂

I submit for your approval: terrible ideas only.

"MIT License to Kill"
"Rebase Another Day"
"The Dev Who Reviewed Me"

Journals and publishers crack down on research from open health data sets PLOS, Frontiers, and others announce policies trying to stem the tide of suspect research

yes - there is certainly an uptick in fairly simple analyses. we've always had a policy excluding simple analyses (BLAST search etc) but what counts as simple is tricky to define and LLMs make a lot of things more simple to do... Others are seeing this too www.science.org/content/arti...

The dilemma is usually: do you want this to be a 2min or a 5 hours conversation?

A lot of computational biology relies on reusing publicly available data. I guess it’s probably easy to automatically generate a bunch of boiler plate analyses and write a manuscript with LLMs as well. Have you seen an uptick akin to this? Do you think it will be a significant problem?

a man in a suit and sunglasses is standing in front of a green screen with a skeleton . ALT: a man in a suit and sunglasses is standing in front of a green screen with a skeleton .

Have you considered this:

Write R, ask Claude code to port it to the other language 🤪

Then I am biased towards tidyverse, but I think it’s nice to do "here is how you would do it in base R"

The way I was "brought up" in this: if you have no programming experience, you should not start with R from scratch but take a basic programming course first. I went through the CS50 course, did a bit of bash, python. And I think that was good background to have before diving into R.

I mean, it's completely fine to say there's a 95% chance that a tibble will not behave as a data frame.

(you can't deny that this was an epic example, incorporating baseR-tidyverse flamewar with frequentist-CI-interpretation-controversial)

Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!

Connecting to some recent threads here:

I wrote something. I hope it can be the start of more conversations about AI and the choices we all have to make.
erincikanek.com/the-rumors-o...

A screenshot of two reply messages on bluesky commenting on the same post. The reply on top is very negative about the data.table package, saying 'it was just the worst'. The bottom reply instead claims that data.table's syntax is the best thing produced in #rstats.

Never change #rstats, never change

Biological Laboratory | LEGO® Ideas This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...

This is (obviously) a step in the right direction: you should share all the code that led to the results (even if you think there is nothing "new" in your code). But who will review the code sharing?

> d3.js code with animations, but "vibe coding" scientific apps is likely to be very dangerous. I would need to completely gut this app of the backend stats functions and substitute my own.

a cartoon of two spidermans standing in front of a nypd van ALT: a cartoon of two spidermans standing in front of a nypd van

Also, mandatory spidy meme

Could it be that they submitted back to back and reviewers asked for replications with eachothers datasets?

It’s true that I cannot count the number of university-linked websites that go down after a few years. But without getting too fancy, a static website hosted on github pages does wonders.

It seems to boil down to the enthusiasm of the authors to make all the work they’ve done accessible when all theses « details » could not fit in the main manuscript

I don’t know about living articles. But for computational work, I deeply appreciate the extended results/methods/discussions that end up buried in the supplementary figures. Sadly they get to live as static pdf when we could have much more engaging interactive formats.

I’m curious as to where you practically run the dev with all that? I’m afraid of letting copilot go wild on my laptop or even more on hpc. I was thinking of containers for this kind of things. Or I don’t know if you can do all that on GitHub directly?

You start with loop, then you get into lapply, finally your discover map. Practice makes purrrfect